Merge branch 'audit-fixes'

.env.example

@@ -1,9 +1,19 @@
 # Copy this file to .env and fill in the values.
 # .env is gitignored — never commit it.
 #
-# Used by `make deploy` to push to GitHub before rsyncing to the VPS.
+# `make deploy` rsyncs the built _site/ to the VPS, then pushes the
-# If either variable is unset, the push step is skipped (rsync still runs).
+# repository to GitHub. The Makefile aborts with a clear error if any
+# of VPS_USER / VPS_HOST / VPS_PATH is unset.
 
+# --- VPS deployment target -------------------------------------------------
+# SSH user on the deployment VPS.
+VPS_USER=
+# Hostname or IP of the deployment VPS.
+VPS_HOST=
+# Absolute path to the document root on the VPS (e.g. /var/www/levineuwirth.org).
+VPS_PATH=
+
+# --- GitHub mirror push ----------------------------------------------------
 # A GitHub fine-grained personal access token with Contents: read+write
 # on the levineuwirth.org repository.
 # Generate at: https://github.com/settings/tokens

.gitignore

@@ -9,6 +9,38 @@ _cache/
 *.swp
 *.swo
 
+# Python bytecode caches
+**/__pycache__/
+*.pyc
+*.pyo
+
+# LaTeX build artifacts (sitewide — covers paper/, any future TeX sources)
+*.aux
+*.bbl
+*.blg
+*.brf
+*.fdb_latexmk
+*.fls
+*.glo
+*.gls
+*.idx
+*.ilg
+*.ind
+*.lof
+*.lot
+*.nav
+*.out
+*.snm
+*.synctex.gz
+*.toc
+*.vrb
+# PGF/TikZ scratch outputs
+pgftest*.pdf
+pgftest*.log
+pgftest*.aux
+# LaTeX run logs (scoped to paper/ — bare *.log would be too broad sitewide)
+paper/*.log
+
 # Data files that are generated at build time (not version-controlled)
 data/embeddings.json
 data/similar-links.json

Makefile

@@ -6,6 +6,12 @@
 export
 
 build:
+	# Auto-snapshot any uncommitted content/ changes BEFORE the build
+	# so the stability heuristic in build/Stability.hs sees a stable
+	# git history. If a subsequent step fails, the snapshot remains in
+	# the history — that's intentional. The next successful build
+	# either reuses it (no new content/ changes) or appends another
+	# snapshot on top, so failures don't disappear from the log.
 	@git add content/
 	@git diff --cached --quiet || git commit -m "auto: $$(date -u +%Y-%m-%dT%H:%M:%SZ)"
 	@date +%s > data/build-start.txt
@@ -54,15 +60,23 @@ pdf-thumbs:
 	fi
 
 deploy: clean build sign
-	git push -u origin main
+	@test -n "$(VPS_USER)" || (echo "deploy: VPS_USER not set in .env" >&2; exit 1)
+	@test -n "$(VPS_HOST)" || (echo "deploy: VPS_HOST not set in .env" >&2; exit 1)
+	@test -n "$(VPS_PATH)" || (echo "deploy: VPS_PATH not set in .env" >&2; exit 1)
 	rsync -avz --delete _site/ $(VPS_USER)@$(VPS_HOST):$(VPS_PATH)/
+	git push -u origin main
 
+watch: export SITE_ENV = dev
 watch:
 	cabal run site -- watch
 
 clean:
 	cabal run site -- clean
 
+# Dev build includes any in-progress drafts under content/drafts/essays/.
+# SITE_ENV=dev is read by build/Site.hs; drafts are otherwise invisible to
+# every build (make build / make deploy / cabal run site -- build directly).
+dev: export SITE_ENV = dev
 dev:
 	cabal run site -- clean
 	cabal run site -- build

README.md

@@ -1 +1,86 @@
 # levineuwirth.org
+
+Personal site of Levi Neuwirth — essays, blog posts, poetry, fiction, and music.
+Built with [Hakyll](https://jaspervdj.be/hakyll/) and [Pandoc](https://pandoc.org/),
+with a custom build system in `build/` and a Haskell + JS + Python toolchain.
+
+## Quickstart
+
+```sh
+make build              # one-shot production build into _site/
+make dev                # dev build (drafts visible) + local server on :8000
+make watch              # cabal-watch rebuild (drafts visible)
+make clean              # cabal run site -- clean
+make deploy             # clean → build → sign → push → rsync to VPS
+```
+
+`make build` always runs `make clean` implicitly when invoked from `make deploy`.
+For day-to-day work, prefer `make dev` (which serves the site on
+`http://localhost:8000`) or `make watch` (rebuilds on save without a server).
+
+**Run `make build` any time you add or replace binary assets** (JPEG/PNG
+figures, PDFs, music assets). `make dev` and `make watch` skip the
+`convert-images.sh` / `pdf-thumbs` preprocessing steps, so a fresh JPEG
+will have no `.webp` companion and a fresh PDF will have no thumbnail
+until a full `make build` regenerates them. Once the companions exist
+they survive subsequent `make dev` runs.
+
+## Optional features
+
+- **Similar-links and embeddings.** `tools/embed.py` precomputes
+  page-level embeddings for the "Related" block. To enable:
+
+  ```sh
+  uv sync                 # creates .venv with sentence-transformers, faiss-cpu
+  ```
+
+  The build silently skips embedding when `.venv` is absent.
+
+- **Client-side semantic search.** Downloads a quantized ONNX model
+  used by `static/js/semantic-search.js` (run once; files are gitignored):
+
+  ```sh
+  make download-model
+  ```
+
+- **Image conversion.** `make build` calls `tools/convert-images.sh` to
+  produce `.webp` companions next to every JPEG/PNG. Requires `cwebp`
+  (`libwebp` on Arch, `webp` on Debian/Ubuntu).
+
+- **PDF thumbnails.** `make pdf-thumbs` generates first-page thumbnails
+  for PDFs in `static/papers/` using `pdftoppm` (`poppler` on Arch,
+  `poppler-utils` on Debian/Ubuntu). Skipped silently when missing.
+
+## Configuration
+
+`.env` (gitignored, copy from `.env.example`) holds the GitHub PAT and
+the VPS rsync target consumed by `make deploy`. Never commit it.
+
+## Repository layout
+
+- `build/` — Haskell build system (Hakyll rules, Pandoc filters, contexts).
+  See `build/Filters/` for the Pandoc AST transforms (sidenotes,
+  wikilinks, transclusion, score embedding, viz, …).
+- `content/` — authored Markdown (essays, blog, poetry, fiction, music).
+- `templates/` — Hakyll/Pandoc HTML templates.
+- `static/` — CSS, JS, fonts, images, vendored PDF.js.
+- `tools/` — Python tooling (embeddings, importers) and shell scripts.
+- `data/` — generated and source data (commonplace.yaml, annotations.json,
+  bibliographies, similar-links.json).
+- `paper/` — LaTeX source for in-progress academic papers.
+- `spec.md` — full architectural notes and design intent.
+
+## Architecture pointers
+
+- `build/Site.hs` is the Hakyll rules entry point.
+- `build/Patterns.hs` defines canonical content patterns shared by
+  Backlinks, Authors, Tags, and Site.
+- `build/Compilers.hs` wires the Pandoc filter chain into Hakyll.
+- `build/Filters/Images.hs` does WebP `<picture>` wrapping; requires
+  the `.webp` companions produced by `tools/convert-images.sh`.
+
+For deeper architectural detail, see `spec.md`.
+
+## License
+
+See `LICENSE`.

build/Authors.hs

@@ -12,32 +12,29 @@
 module Authors
     ( buildAllAuthors
     , applyAuthorRules
-    , authorLinksField
     ) where
 
-import Data.Char            (isAlphaNum, toLower)
 import Data.Maybe           (fromMaybe)
 import Hakyll
-import Hakyll.Core.Metadata (lookupStringList)
 import Pagination           (sortAndGroup)
-import Tags                 (tagLinksField)
+import Patterns             (authorIndexable)
+import Contexts             (abstractField, tagLinksField)
+import Utils                (authorSlugify, authorNameOf)
 
 
 -- ---------------------------------------------------------------------------
 -- Slug helpers
+--
+-- The slugify and nameOf helpers used to live here in their own
+-- definitions; they now defer to 'Utils' so that they cannot drift from
+-- the 'Contexts' versions on Unicode edge cases.
 -- ---------------------------------------------------------------------------
 
--- | Lowercase, replace spaces with hyphens, strip anything else.
 slugify :: String -> String
-slugify = map (\c -> if c == ' ' then '-' else c)
+slugify = authorSlugify
-        . filter (\c -> isAlphaNum c || c == ' ')
-        . map toLower
 
--- | Extract the author name from a "Name | url" entry, trimming whitespace.
 nameOf :: String -> String
-nameOf s = strip $ case break (== '|') s of { (n, _) -> n }
+nameOf = authorNameOf
-  where
-    strip = reverse . dropWhile (== ' ') . reverse . dropWhile (== ' ')
 
 
 -- ---------------------------------------------------------------------------
@@ -47,8 +44,10 @@ nameOf s = strip $ case break (== '|') s of { (n, _) -> n }
 defaultAuthor :: String
 defaultAuthor = "Levi Neuwirth"
 
+-- | Content patterns indexed by author. Sourced from 'Patterns.authorIndexable'
+-- so this stays in lockstep with Tags.hs and Backlinks.hs.
 allContent :: Pattern
-allContent = ("content/essays/*.md" .||. "content/blog/*.md") .&&. hasNoVersion
+allContent = authorIndexable
 
 
 -- ---------------------------------------------------------------------------
@@ -103,25 +102,7 @@ applyAuthorRules authors baseCtx = tagsRules authors $ \name pat -> do
   where
     itemCtx = dateField "date" "%-d %B %Y"
            <> tagLinksField "item-tags"
+           <> abstractField
            <> defaultContext
 
 
--- ---------------------------------------------------------------------------
--- Context field
--- ---------------------------------------------------------------------------
-
--- | Exposes each item's authors as @author-name@ / @author-url@ pairs.
---   All links point to /authors/{slug}/, regardless of any URL in frontmatter.
---   Defaults to Levi Neuwirth when no "authors" frontmatter key is present.
---
---   Usage in templates:
---     $for(author-links)$<a href="$author-url$">$author-name$</a>$sep$, $endfor$
-authorLinksField :: Context a
-authorLinksField = listFieldWith "author-links" ctx $ \item -> do
-    meta <- getMetadata (itemIdentifier item)
-    let entries = fromMaybe [] (lookupStringList "authors" meta)
-        names   = if null entries then [defaultAuthor] else map nameOf entries
-    return $ map (\n -> Item (fromFilePath "") (n, "/authors/" ++ slugify n ++ "/")) names
-  where
-    ctx = field "author-name" (return . fst . itemBody)
-       <> field "author-url"  (return . snd . itemBody)

build/Backlinks.hs

@@ -32,10 +32,12 @@ import           Data.Ord                   (comparing)
 import           Data.Maybe                 (fromMaybe)
 import qualified Data.Map.Strict            as Map
 import           Data.Map.Strict            (Map)
+import qualified Data.ByteString            as BS
 import qualified Data.Text                  as T
 import qualified Data.Text.Lazy             as TL
 import qualified Data.Text.Lazy.Encoding    as TLE
 import qualified Data.Text.Encoding         as TE
+import qualified Data.Text.Encoding.Error   as TE
 import qualified Data.Aeson                 as Aeson
 import           Data.Aeson                 ((.=))
 import           Text.Pandoc.Class          (runPure)
@@ -47,6 +49,7 @@ import           Text.Pandoc.Walk           (query)
 import           Hakyll
 import           Compilers                  (readerOpts, writerOpts)
 import           Filters                    (preprocessSource)
+import qualified Patterns                   as P
 
 -- ---------------------------------------------------------------------------
 -- Link-with-context entry (intermediate, saved by the "links" pass)
@@ -184,28 +187,47 @@ linksCompiler = do
 -- ---------------------------------------------------------------------------
 
 -- | Normalise an internal URL as a map key: strip query string, fragment,
--- and trailing @.html@; ensure a leading slash.
+-- and trailing @.html@; ensure a leading slash; percent-decode the path
+-- so that @\/essays\/caf%C3%A9@ and @\/essays\/café@ collide on the same
+-- key.
 normaliseUrl :: String -> String
 normaliseUrl url =
     let t  = T.pack url
         t1 = fst (T.breakOn "?" (fst (T.breakOn "#" t)))
         t2 = if T.isPrefixOf "/" t1 then t1 else "/" `T.append` t1
         t3 = fromMaybe t2 (T.stripSuffix ".html" t2)
-    in  T.unpack t3
+    in  percentDecode (T.unpack t3)
+
+-- | Decode percent-escapes (@%XX@) into raw bytes, then re-interpret the
+-- resulting bytestring as UTF-8. Invalid escapes are passed through
+-- verbatim so this is safe to call on already-decoded input.
+percentDecode :: String -> String
+percentDecode = T.unpack . TE.decodeUtf8With lenientDecode . pack . go
+  where
+    go []                 = []
+    go ('%':a:b:rest)
+        | Just hi <- hexDigit a
+        , Just lo <- hexDigit b
+        = fromIntegral (hi * 16 + lo) : go rest
+    go (c:rest)           = fromIntegral (fromEnum c) : go rest
+
+    hexDigit c
+        | c >= '0' && c <= '9' = Just (fromEnum c - fromEnum '0')
+        | c >= 'a' && c <= 'f' = Just (fromEnum c - fromEnum 'a' + 10)
+        | c >= 'A' && c <= 'F' = Just (fromEnum c - fromEnum 'A' + 10)
+        | otherwise            = Nothing
+
+    pack = BS.pack
+    lenientDecode = TE.lenientDecode
 
 -- ---------------------------------------------------------------------------
--- Content patterns (must match the rules in Site.hs)
+-- Content patterns (must match the rules in Site.hs — sourced from
+-- Patterns.allContent so additions to the canonical list automatically
+-- propagate to backlinks).
 -- ---------------------------------------------------------------------------
 
 allContent :: Pattern
-allContent =
+allContent = P.allContent
-       "content/essays/*.md"
-  .||. "content/essays/*/index.md"
-  .||. "content/blog/*.md"
-  .||. "content/poetry/*.md"
-  .||. "content/fiction/*.md"
-  .||. "content/music/*/index.md"
-  .||. "content/*.md"
 
 -- ---------------------------------------------------------------------------
 -- Hakyll rules

build/Catalog.hs

@@ -7,7 +7,8 @@ module Catalog
     ( musicCatalogCtx
     ) where
 
-import Data.List     (groupBy, sortBy)
+import Data.Char     (isSpace, toLower)
+import Data.List     (groupBy, isPrefixOf, sortBy)
 import Data.Maybe    (fromMaybe)
 import Data.Ord      (comparing)
 import Data.Aeson    (Value (..))
@@ -15,7 +16,6 @@ import qualified Data.Aeson.KeyMap as KM
 import qualified Data.Vector       as V
 import qualified Data.Text         as T
 import Hakyll
-import Hakyll.Core.Metadata (lookupStringList)
 import Contexts (siteCtx)
 
 -- ---------------------------------------------------------------------------
@@ -115,6 +115,40 @@ parseCatalogEntry item = do
 -- ---------------------------------------------------------------------------
 -- HTML rendering
 -- ---------------------------------------------------------------------------
+--
+-- Trust model: per the site convention (see also Stats.hs:pageLink),
+-- frontmatter @title@ values are author-controlled trusted HTML and may
+-- contain inline markup such as @<em>...</em>@. They are emitted
+-- pre-escaped — but we still escape every other interpolated frontmatter
+-- value (year, duration, instrumentation) and sanitize hrefs through
+-- 'safeHref', so a stray @<@ in those fields cannot break the markup.
+
+-- | Defense-in-depth href sanitiser. Mirrors 'Stats.isSafeUrl'.
+safeHref :: String -> String
+safeHref u =
+    let norm = map toLower (dropWhile isSpace u)
+    in  if not ("//" `isPrefixOf` norm)
+           && any (`isPrefixOf` norm) ["/", "https://", "mailto:", "#"]
+        then escAttr u
+        else "#"
+
+escAttr :: String -> String
+escAttr = concatMap esc
+  where
+    esc '&'  = "&amp;"
+    esc '<'  = "&lt;"
+    esc '>'  = "&gt;"
+    esc '"'  = "&quot;"
+    esc '\'' = "&#39;"
+    esc c    = [c]
+
+escText :: String -> String
+escText = concatMap esc
+  where
+    esc '&' = "&amp;"
+    esc '<' = "&lt;"
+    esc '>' = "&gt;"
+    esc c   = [c]
 
 renderIndicators :: CatalogEntry -> String
 renderIndicators e = concatMap render
@@ -129,19 +163,21 @@ renderEntry :: CatalogEntry -> String
 renderEntry e = concat
     [ "<li class=\"catalog-entry\">"
     ,   "<div class=\"catalog-entry-main\">"
-    ,     "<a class=\"catalog-title\" href=\"", ceUrl e, "\">", ceTitle e, "</a>"
+    ,     "<a class=\"catalog-title\" href=\"", safeHref (ceUrl e), "\">"
+    ,       ceTitle e
+    ,     "</a>"
     ,     renderIndicators e
-    ,     maybe "" (\y -> "<span class=\"catalog-year\">" ++ y ++ "</span>") (ceYear e)
+    ,     maybe "" (\y -> "<span class=\"catalog-year\">" ++ escText y ++ "</span>") (ceYear e)
-    ,     maybe "" (\d -> "<span class=\"catalog-duration\">" ++ d ++ "</span>") (ceDuration e)
+    ,     maybe "" (\d -> "<span class=\"catalog-duration\">" ++ escText d ++ "</span>") (ceDuration e)
     ,   "</div>"
-    ,   maybe "" (\i -> "<div class=\"catalog-instrumentation\">" ++ i ++ "</div>") (ceInstrumentation e)
+    ,   maybe "" (\i -> "<div class=\"catalog-instrumentation\">" ++ escText i ++ "</div>") (ceInstrumentation e)
     , "</li>"
     ]
 
 renderCategorySection :: String -> [CatalogEntry] -> String
 renderCategorySection cat entries = concat
     [ "<section class=\"catalog-section\">"
-    ,   "<h2 class=\"catalog-section-title\">", categoryLabel cat, "</h2>"
+    ,   "<h2 class=\"catalog-section-title\">", escText (categoryLabel cat), "</h2>"
     ,   "<ul class=\"catalog-list\">"
     ,   concatMap renderEntry entries
     ,   "</ul>"
@@ -191,7 +227,12 @@ catalogByCategoryField = field "catalog-by-category" $ \_ -> do
         else do
             let sorted  = sortBy (comparing (categoryRank . ceCategory)) entries
                 grouped = groupBy (\a b -> ceCategory a == ceCategory b) sorted
-            return $ concatMap (\g -> renderCategorySection (ceCategory (head g)) g) grouped
+            return $ concatMap renderGroup grouped
+  where
+    -- groupBy on a non-empty list yields non-empty sublists, but pattern
+    -- matching is total whereas 'head' is not.
+    renderGroup []        = ""
+    renderGroup g@(e : _) = renderCategorySection (ceCategory e) g
 
 musicCatalogCtx :: Context String
 musicCatalogCtx =

build/Citations.hs

@@ -137,9 +137,14 @@ transformInline :: Map Text Int -> Inline -> Inline
 transformInline keyNums (Cite citations _) =
     let keys = map citationId citations
         nums = mapMaybe (`Map.lookup` keyNums) keys
-    in if null nums
+    in case (keys, nums) of
-           then Str ""
+        -- Both lists are guaranteed non-empty by the @null nums@ check
-           else RawInline "html" (markerHtml keys (head keys) (head nums) nums)
+        -- below, but pattern-match to keep this total instead of
+        -- relying on @head@.
+        (firstKey : _, firstNum : _) ->
+            RawInline "html" (markerHtml keys firstKey firstNum nums)
+        _ ->
+            Str ""
 transformInline _ x = x
 
 markerHtml :: [Text] -> Text -> Int -> [Int] -> Text

build/Commonplace.hs

@@ -125,9 +125,9 @@ renderThemedView entries =
 renderChronoView :: [CPEntry] -> String
 renderChronoView entries =
     "<div class=\"cp-chrono\" id=\"cp-chrono\" hidden>"
-    ++ if null sorted
+    ++ (if null sorted
-        then "<p class=\"cp-empty\">No entries yet.</p>"
+            then "<p class=\"cp-empty\">No entries yet.</p>"
-        else concatMap renderEntry sorted
+            else concatMap renderEntry sorted)
     ++ "</div>"
   where
     sorted = sortBy (comparing (Down . cpDateAdded)) entries

build/Compilers.hs

@@ -12,7 +12,6 @@ module Compilers
     ) where
 
 import           Hakyll
-import           Hakyll.Core.Metadata       (lookupStringList, lookupString)
 import           Text.Pandoc.Definition     (Pandoc (..), Block (..),
                                              Inline (..))
 import           Text.Pandoc.Options        (ReaderOptions (..), WriterOptions (..),
@@ -158,7 +157,9 @@ essayCompilerWith rOpts = do
         Viz.inlineViz srcDir pandocWithScores
 
     -- Apply remaining AST-level filters (sidenotes, smallcaps, links, etc.).
-    let pandocFiltered = applyAll pandocWithViz
+    -- applyAll touches the filesystem via Images.apply (webp existence
+    -- check), so it runs through unsafeCompiler.
+    pandocFiltered <- unsafeCompiler $ applyAll srcDir pandocWithViz
     let pandocItem'    = itemSetBody pandocFiltered pandocItem
 
     -- Build TOC from the filtered AST.
@@ -205,8 +206,12 @@ pageCompiler = do
     body <- getResourceBody
     let src   = itemBody body
         body' = itemSetBody (preprocessSource src) body
-    pandocItem <- fmap (fmap applyAll) (readPandocWith readerOpts body')
+    filePath   <- getResourceFilePath
-    let htmlItem = writePandocWith writerOpts pandocItem
+    let srcDir  = takeDirectory filePath
+    pandocItem <- readPandocWith readerOpts body'
+    pandocFiltered <- unsafeCompiler $ applyAll srcDir (itemBody pandocItem)
+    let pandocItem' = itemSetBody pandocFiltered pandocItem
+    let htmlItem    = writePandocWith writerOpts pandocItem'
     _ <- saveSnapshot "word-count"   (itemSetBody (show (wordCount src))   htmlItem)
     _ <- saveSnapshot "reading-time" (itemSetBody (show (readingTime src)) htmlItem)
     return htmlItem

build/Contexts.hs

@@ -9,13 +9,16 @@ module Contexts
     , fictionCtx
     , compositionCtx
     , contentKindField
+    , abstractField
+    , tagLinksField
+    , authorLinksField
     ) where
 
 import Data.Aeson              (Value (..))
 import qualified Data.Aeson.KeyMap  as KM
 import qualified Data.Vector        as V
-import Data.List               (isPrefixOf)
+import Data.List               (intercalate, isPrefixOf)
-import Data.Maybe              (catMaybes, fromMaybe)
+import Data.Maybe              (fromMaybe)
 import Data.Time.Calendar      (toGregorian)
 import Data.Time.Clock         (getCurrentTime, utctDay)
 import Data.Time.Format        (formatTime, defaultTimeLocale)
@@ -24,13 +27,11 @@ import Text.Read               (readMaybe)
 import qualified Data.Text     as T
 import Text.Pandoc             (runPure, readMarkdown, writeHtml5String, Pandoc(..), Block(..), Inline(..))
 import Text.Pandoc.Options     (WriterOptions(..), HTMLMathMethod(..))
-import Hakyll
+import Hakyll       hiding (trim)
-import Hakyll.Core.Metadata    (lookupStringList)
-import Authors      (authorLinksField)
 import Backlinks    (backlinksField)
 import SimilarLinks (similarLinksField)
 import Stability    (stabilityField, lastReviewedField, versionHistoryField)
-import Tags       (tagLinksField)
+import Utils        (authorSlugify, authorNameOf, trim)
 
 -- ---------------------------------------------------------------------------
 -- Affiliation field
@@ -96,13 +97,13 @@ contentKindField = field "item-kind" $ \item -> do
     r <- getRoute (itemIdentifier item)
     return $ case r of
         Nothing -> "Page"
-        Just route
+        Just r'
-            | "essays/"  `isPrefixOf` route -> "Essay"
+            | "essays/"  `isPrefixOf` r' -> "Essay"
-            | "blog/"    `isPrefixOf` route -> "Post"
+            | "blog/"    `isPrefixOf` r' -> "Post"
-            | "poetry/"  `isPrefixOf` route -> "Poem"
+            | "poetry/"  `isPrefixOf` r' -> "Poem"
-            | "fiction/" `isPrefixOf` route -> "Fiction"
+            | "fiction/" `isPrefixOf` r' -> "Fiction"
-            | "music/"   `isPrefixOf` route -> "Composition"
+            | "music/"   `isPrefixOf` r' -> "Composition"
-            | otherwise                      -> "Page"
+            | otherwise                   -> "Page"
 
 -- ---------------------------------------------------------------------------
 -- Site-wide context
@@ -112,22 +113,79 @@ contentKindField = field "item-kind" $ \item -> do
 -- in the @js:@ frontmatter key (accepts a scalar string or a YAML list).
 -- Returns an empty list when absent; $for iterates zero times, emitting nothing.
 -- NOTE: do not use fail here — $for does not catch noResult the way $if does.
+--
+-- Each child Item is keyed on @<parent-identifier>#js-<index>@ so that two
+-- pages referencing the same script path (e.g. @shared.js@) do not collide
+-- in Hakyll's item store.
 pageScriptsField :: Context String
 pageScriptsField = listFieldWith "page-scripts" ctx $ \item -> do
     meta <- getMetadata (itemIdentifier item)
     let scripts = case lookupStringList "js" meta of
                     Just xs -> xs
                     Nothing -> maybe [] (:[]) (lookupString "js" meta)
-    return $ map (\s -> Item (fromFilePath s) s) scripts
+        parent  = toFilePath (itemIdentifier item)
+    return $ zipWith
+        (\i s -> Item (fromFilePath (parent ++ "#js-" ++ show (i :: Int))) s)
+        [0 ..]
+        scripts
   where
     ctx = field "script-src" (return . itemBody)
 
+-- ---------------------------------------------------------------------------
+-- Tag links field
+-- ---------------------------------------------------------------------------
+
+-- | List context field exposing an item's own (non-expanded) tags as
+--   @tag-name@ / @tag-url@ objects.
+--
+--   $for(essay-tags)$<a href="$tag-url$">$tag-name$</a>$endfor$
+tagLinksField :: String -> Context a
+tagLinksField fieldName = listFieldWith fieldName ctx $ \item ->
+    map toItem <$> getTags (itemIdentifier item)
+  where
+    toItem t = Item (fromFilePath (t ++ "/index.html")) t
+    ctx      = field "tag-name" (return . itemBody)
+            <> field "tag-url"  (\i -> return $ "/" ++ itemBody i ++ "/")
+
+-- ---------------------------------------------------------------------------
+-- Author links field
+-- ---------------------------------------------------------------------------
+--
+-- 'authorSlugify' and 'authorNameOf' are imported from 'Utils' so that
+-- they cannot drift from the copies in 'Authors'.
+
+-- | Exposes each item's authors as @author-name@ / @author-url@ pairs.
+--   Defaults to Levi Neuwirth when no "authors" frontmatter key is present.
+--
+--   Entries that produce an empty name (e.g. @"| https://url"@) or an empty
+--   slug (e.g. all-punctuation names) are dropped, so the field never emits
+--   a @/authors//@ link.
+--
+--   $for(author-links)$<a href="$author-url$">$author-name$</a>$sep$, $endfor$
+authorLinksField :: Context a
+authorLinksField = listFieldWith "author-links" ctx $ \item -> do
+    meta <- getMetadata (itemIdentifier item)
+    let entries = fromMaybe [] (lookupStringList "authors" meta)
+        rawNames = if null entries then ["Levi Neuwirth"] else map authorNameOf entries
+        validNames = filter (\n -> not (null n) && not (null (authorSlugify n))) rawNames
+        names = if null validNames then ["Levi Neuwirth"] else validNames
+    return $ map (\n -> Item (fromFilePath "") (n, "/authors/" ++ authorSlugify n ++ "/")) names
+  where
+    ctx = field "author-name" (return . fst . itemBody)
+       <> field "author-url"  (return . snd . itemBody)
+
 -- ---------------------------------------------------------------------------
 -- Abstract field
 -- ---------------------------------------------------------------------------
 
 -- | Renders the abstract using Pandoc to support Markdown and LaTeX math.
---   Strips the outer <p> tag if the abstract is a single paragraph.
+--   Strips the outer @<p>@ wrapping. A single-paragraph abstract becomes a
+--   bare @Plain@ so the rendered HTML is unwrapped inlines. A multi-paragraph
+--   abstract (author used a blank line in the YAML literal block) is flattened
+--   to a single @Plain@ with @LineBreak@ separators between what were
+--   originally paragraph boundaries — the visual break is preserved without
+--   emitting stray @<p>@ tags inside the metadata block. Mixed block content
+--   (e.g. an abstract containing a blockquote) falls through unchanged.
 abstractField :: Context String
 abstractField = field "abstract" $ \item -> do
     meta <- getMetadata (itemIdentifier item)
@@ -138,12 +196,20 @@ abstractField = field "abstract" $ \item -> do
                     doc <- readMarkdown defaultHakyllReaderOptions (T.pack src)
                     let doc' = case doc of
                                  Pandoc m [Para ils] -> Pandoc m [Plain ils]
-                                 _                   -> doc
+                                 Pandoc m blocks
+                                   | all isPara blocks && not (null blocks) ->
+                                       let joined = intercalate [LineBreak]
+                                                      [ils | Para ils <- blocks]
+                                       in Pandoc m [Plain joined]
+                                 _ -> doc
                     let wOpts = defaultHakyllWriterOptions { writerHTMLMathMethod = MathML }
                     writeHtml5String wOpts doc'
             case pandocResult of
                 Left err -> fail $ "Pandoc error rendering abstract: " ++ show err
                 Right html -> return (T.unpack html)
+  where
+    isPara (Para _) = True
+    isPara _        = False
 
 siteCtx :: Context String
 siteCtx =
@@ -208,21 +274,37 @@ dotsField ctxKey metaKey = field ctxKey $ \item -> do
 -- | @$confidence-trend$@: ↑, ↓, or → derived from the last two entries
 -- in the @confidence-history@ frontmatter list.  Returns @noResult@ when
 -- there is no history or only a single entry.
+--
+-- The arrow flips when the absolute change crosses 'trendThreshold'
+-- (currently 5 percentage points). Smaller swings count as flat.
 confidenceTrendField :: Context String
 confidenceTrendField = field "confidence-trend" $ \item -> do
     meta <- getMetadata (itemIdentifier item)
     case lookupStringList "confidence-history" meta of
-        Nothing                -> fail "no confidence history"
+        Nothing -> fail "no confidence history"
-        Just xs | length xs < 2 -> fail "no confidence history"
+        Just xs -> case lastTwo xs of
-        Just xs ->
+            Nothing            -> fail "no confidence history"
-            let prev = readMaybe (xs !! (length xs - 2)) :: Maybe Int
+            Just (prevS, curS) ->
-                cur  = readMaybe (last xs)               :: Maybe Int
+                let prev = readMaybe prevS :: Maybe Int
-            in  case (prev, cur) of
+                    cur  = readMaybe curS  :: Maybe Int
-                    (Just p, Just c)
+                in  case (prev, cur) of
-                        | c - p >  5 -> return "\x2191"   -- ↑
+                        (Just p, Just c)
-                        | p - c >  5 -> return "\x2193"   -- ↓
+                            | c - p >  trendThreshold -> return "\x2191"   -- ↑
-                        | otherwise  -> return "\x2192"   -- →
+                            | p - c >  trendThreshold -> return "\x2193"   -- ↓
-                    _ -> return "\x2192"
+                            | otherwise               -> return "\x2192"   -- →
+                        _ -> return "\x2192"
+  where
+    trendThreshold :: Int
+    trendThreshold = 5
+
+    -- Total replacement for @(xs !! (length xs - 2), last xs)@: returns
+    -- the last two elements of a list, in order, or 'Nothing' when the
+    -- list has fewer than two entries.
+    lastTwo :: [a] -> Maybe (a, a)
+    lastTwo []        = Nothing
+    lastTwo [_]       = Nothing
+    lastTwo [a, b]    = Just (a, b)
+    lastTwo (_ : rest) = lastTwo rest
 
 -- | @$overall-score$@: weighted composite of confidence (50 %),
 --   evidence quality (30 %), and importance (20 %), expressed as an
@@ -332,12 +414,27 @@ data Movement = Movement
     , movAudio    :: Maybe String
     }
 
-parseMovements :: Metadata -> [Movement]
+-- | Parse the @movements@ frontmatter key. Returns parsed movements and a
-parseMovements meta =
+--   list of human-readable warnings for any entries that failed to parse.
+--   Callers can surface the warnings via 'unsafeCompiler' so silent typos
+--   don't strip movements without diagnostic.
+parseMovementsWithWarnings :: Metadata -> ([Movement], [String])
+parseMovementsWithWarnings meta =
     case KM.lookup "movements" meta of
-        Just (Array v) -> catMaybes $ map parseOne (V.toList v)
+        Just (Array v) ->
-        _              -> []
+            let results = zipWith parseIndexed [1 :: Int ..] (V.toList v)
+            in  ( [m | Right m <- results]
+                , [w | Left  w <- results]
+                )
+        _ -> ([], [])
   where
+    parseIndexed i value =
+        case parseOne value of
+            Just m  -> Right m
+            Nothing -> Left $
+                "movement #" ++ show i ++ " is missing a required field "
+                ++ "(name, page, or duration) — entry skipped"
+
     parseOne (Object o) = Movement
         <$> (getString =<< KM.lookup "name"     o)
         <*> (getInt    =<< KM.lookup "page"     o)
@@ -351,6 +448,9 @@ parseMovements meta =
     getInt (Number n) = Just (floor (fromRational (toRational n) :: Double))
     getInt _          = Nothing
 
+parseMovements :: Metadata -> [Movement]
+parseMovements = fst . parseMovementsWithWarnings
+
 -- | Extract the composition slug from an item's identifier.
 --   "content/music/symphonic-dances/index.md" → "symphonic-dances"
 compSlug :: Item a -> String
@@ -410,7 +510,11 @@ compositionCtx =
 
     movementsListField = listFieldWith "movements" movCtx $ \item -> do
         meta <- getMetadata (itemIdentifier item)
-        let mvs = parseMovements meta
+        let (mvs, warnings) = parseMovementsWithWarnings meta
+            ident = toFilePath (itemIdentifier item)
+        unsafeCompiler $ mapM_
+            (\w -> putStrLn $ "[Movements] " ++ ident ++ ": " ++ w)
+            warnings
         return $ zipWith
             (\idx mv -> Item (fromFilePath ("mv" ++ show (idx :: Int))) mv)
             [1..] mvs

build/Filters.hs

@@ -22,16 +22,25 @@ import qualified Filters.Images     as Images
 
 -- | Apply all AST-level filters in pipeline order.
 --   Run on the Pandoc document after reading, before writing.
-applyAll :: Pandoc -> Pandoc
+--
-applyAll
+--   'Filters.Images.apply' is the only IO-performing filter (it probes the
-    = Sidenotes.apply
+--   filesystem for @.webp@ companions before deciding whether to emit
-    . Typography.apply
+--   @<picture>@). It runs first — i.e. innermost in the composition — and
-    . Links.apply
+--   every downstream filter stays pure. @srcDir@ is the directory of the
-    . Smallcaps.apply
+--   source Markdown file, passed through to Images for relative-path
-    . Dropcaps.apply
+--   resolution of co-located assets.
-    . Math.apply
+applyAll :: FilePath -> Pandoc -> IO Pandoc
-    . Code.apply
+applyAll srcDir doc = do
-    . Images.apply
+    imagesDone <- Images.apply srcDir doc
+    pure
+        . Sidenotes.apply
+        . Typography.apply
+        . Links.apply
+        . Smallcaps.apply
+        . Dropcaps.apply
+        . Math.apply
+        . Code.apply
+        $ imagesDone
 
 -- | Apply source-level preprocessors to the raw Markdown string.
 --   Order matters: EmbedPdf must run before Transclusion, because the

build/Filters/EmbedPdf.hs

@@ -16,6 +16,7 @@ module Filters.EmbedPdf (preprocess) where
 
 import Data.Char (isDigit)
 import Data.List (isPrefixOf, isSuffixOf)
+import qualified Utils as U
 
 -- | Apply PDF-embed substitution to the raw Markdown source string.
 preprocess :: String -> String
@@ -23,7 +24,7 @@ preprocess = unlines . map processLine . lines
 
 processLine :: String -> String
 processLine line =
-    case parseDirective (trim line) of
+    case parseDirective (U.trim line) of
         Nothing                    -> line
         Just (filePath, pageHash)  -> renderEmbed filePath pageHash
 
@@ -64,7 +65,9 @@ renderEmbed filePath pageHash =
 
 -- | Percent-encode characters that would break a query-string value.
 --   Slashes are left unencoded so root-relative paths remain readable and
---   work correctly with PDF.js's internal fetch.
+--   work correctly with PDF.js's internal fetch.  @#@ is encoded for
+--   defense-in-depth even though the directive parser already splits on it
+--   before this function is called.
 encodeQueryValue :: String -> String
 encodeQueryValue = concatMap enc
   where
@@ -73,9 +76,6 @@ encodeQueryValue = concatMap enc
     enc '?' = "%3F"
     enc '+' = "%2B"
     enc '"' = "%22"
+    enc '#' = "%23"
     enc c   = [c]
 
--- | Strip leading and trailing spaces.
-trim :: String -> String
-trim = f . f
-  where f = reverse . dropWhile (== ' ')

build/Filters/Images.hs

@@ -2,53 +2,93 @@
 {-# LANGUAGE OverloadedStrings #-}
 -- | Image filter: lazy loading, lightbox markers, and WebP <picture> wrappers.
 --
---   For local raster images (JPG, JPEG, PNG, GIF), emits a @<picture>@ element
+--   For local raster images (JPG, JPEG, PNG, GIF) whose @.webp@ companion
---   with a WebP @<source>@ and the original format as the @<img>@ fallback.
+--   exists on disk at build time, emits a @<picture>@ element with a WebP
---   tools/convert-images.sh produces the companion .webp files at build time.
+--   @<source>@ and the original format as the @<img>@ fallback. When the
+--   webp companion is absent (cwebp not installed, @convert-images.sh@ not
+--   yet run, or a single file missed), the filter emits a plain @<img>@ so
+--   the image still renders. This matters because browsers do NOT fall back
+--   from a 404'd @<source>@ inside @<picture>@ to the nested @<img>@ — the
+--   source is selected up front and a broken one leaves the area blank.
+--
+--   @tools/convert-images.sh@ produces the companion .webp files at build
+--   time. When cwebp is not installed the script is a no-op, and this
+--   filter degrades gracefully to plain @<img>@.
 --
 --   SVG files and external URLs are passed through with only lazy loading
 --   (and lightbox markers for standalone images).
 module Filters.Images (apply) where
 
 import           Data.Char            (toLower)
+import           Data.List            (isPrefixOf)
 import           Data.Text            (Text)
 import qualified Data.Text            as T
-import           System.FilePath      (replaceExtension)
+import           System.Directory     (doesFileExist)
+import           System.FilePath      (replaceExtension, takeExtension, (</>))
 import           Text.Pandoc.Definition
-import           Text.Pandoc.Walk     (walk)
+import           Text.Pandoc.Walk     (walkM)
+import qualified Utils                as U
 
 -- | Apply image attribute injection and WebP wrapping to the entire document.
-apply :: Pandoc -> Pandoc
+--
-apply = walk transformInline
+--   @srcDir@ is the directory of the source Markdown file, used to resolve
+--   relative image paths when probing for the corresponding @.webp@
+--   companion file. Absolute paths (leading @/@) are resolved against
+--   @static/@ instead, matching the layout @convert-images.sh@ writes to.
+apply :: FilePath -> Pandoc -> IO Pandoc
+apply srcDir = walkM (transformInline srcDir)
 
 -- ---------------------------------------------------------------------------
 -- Core transformation
 -- ---------------------------------------------------------------------------
 
-transformInline :: Inline -> Inline
+transformInline :: FilePath -> Inline -> IO Inline
-transformInline (Link lAttr ils lTarget) =
+transformInline srcDir (Link lAttr ils lTarget) = do
     -- Recurse into link contents; images inside a link get no lightbox marker.
-    Link lAttr (map wrapLinkedImg ils) lTarget
+    ils' <- mapM (wrapLinkedImg srcDir) ils
-  where
+    pure (Link lAttr ils' lTarget)
-    wrapLinkedImg (Image iAttr alt iTarget) = renderImg iAttr alt iTarget False
+transformInline srcDir (Image attr alt target) =
-    wrapLinkedImg x                         = x
+    renderImg srcDir attr alt target True
-transformInline (Image attr alt target) =
+transformInline _ x = pure x
-    renderImg attr alt target True
+
-transformInline x = x
+wrapLinkedImg :: FilePath -> Inline -> IO Inline
+wrapLinkedImg srcDir (Image iAttr alt iTarget) =
+    renderImg srcDir iAttr alt iTarget False
+wrapLinkedImg _ x = pure x
 
 -- | Dispatch on image type:
---   * Local raster → @<picture>@ with WebP @<source>@
+--   * Local raster with webp companion on disk → @<picture>@ with WebP @<source>@
---   * Everything else → plain @<img>@ with loading/lightbox attrs
+--   * Local raster without companion → plain @<img>@ (graceful degradation)
-renderImg :: Attr -> [Inline] -> Target -> Bool -> Inline
+--   * Everything else (SVG, URL) → plain @<img>@ with loading/lightbox attrs
-renderImg attr alt target@(src, _) lightbox
+renderImg :: FilePath -> Attr -> [Inline] -> Target -> Bool -> IO Inline
-    | isLocalRaster (T.unpack src) =
+renderImg srcDir attr alt target@(src, _) lightbox
-        RawInline (Format "html") (renderPicture attr alt target lightbox)
+    | isLocalRaster (T.unpack src) = do
+        hasWebp <- doesFileExist (webpPhysicalPath srcDir src)
+        if hasWebp
+            then pure $ RawInline (Format "html")
+                                  (renderPicture attr alt target lightbox)
+            else pure $ Image (addLightbox lightbox (addAttr "loading" "lazy" attr))
+                              alt target
     | otherwise =
-        Image (addLightbox lightbox (addAttr "loading" "lazy" attr)) alt target
+        pure $ Image (addLightbox lightbox (addAttr "loading" "lazy" attr)) alt target
   where
     addLightbox True  a = addAttr "data-lightbox" "true" a
     addLightbox False a = a
 
+-- | Physical on-disk path of the @.webp@ companion for a Markdown image src.
+--
+--   Absolute paths (@/images/foo.jpg@) resolve under @static/@ because that
+--   is where Hakyll's static-asset rule writes them from. Relative paths
+--   resolve against the source file's directory, where Pandoc already
+--   expects co-located assets to live.
+webpPhysicalPath :: FilePath -> Text -> FilePath
+webpPhysicalPath srcDir src =
+    let s = T.unpack src
+        physical = if "/" `isPrefixOf` s
+                   then "static" ++ s
+                   else srcDir </> s
+    in replaceExtension physical ".webp"
+
 -- ---------------------------------------------------------------------------
 -- <picture> rendering
 -- ---------------------------------------------------------------------------
@@ -73,8 +113,13 @@ renderPicture (ident, classes, kvs) alt (src, title) lightbox =
         ]
   where
     webpSrc   = replaceExtension (T.unpack src) ".webp"
-    -- Strip attrs we handle explicitly so they don't appear twice.
+    -- Strip attrs we handle explicitly above (id/class/alt/title) and the
-    passedKvs = filter (\(k, _) -> k `notElem` ["loading", "data-lightbox"]) kvs
+    -- attrs we always emit ourselves (loading, data-lightbox), so they don't
+    -- appear twice on the <img>.
+    passedKvs = filter
+        (\(k, _) -> k `notElem`
+            ["loading", "data-lightbox", "id", "class", "alt", "title", "src"])
+        kvs
 
 attrId :: Text -> Text
 attrId t = if T.null t then "" else " id=\"" <> esc t <> "\""
@@ -103,11 +148,11 @@ isLocalRaster src = not (isUrl src) && lowerExt src `elem` [".jpg", ".jpeg", ".p
 
 isUrl :: String -> Bool
 isUrl s = any (`isPrefixOf` s) ["http://", "https://", "//", "data:"]
-  where isPrefixOf pfx str = take (length pfx) str == pfx
 
 -- | Extension of a path, lowercased (e.g. ".JPG" → ".jpg").
+--   Returns the empty string for paths with no extension.
 lowerExt :: FilePath -> String
-lowerExt = map toLower . reverse . ('.' :) . takeWhile (/= '.') . tail . dropWhile (/= '.') . reverse
+lowerExt = map toLower . takeExtension
 
 -- | Prepend a key=value pair if not already present.
 addAttr :: Text -> Text -> Attr -> Attr
@@ -119,24 +164,28 @@ addAttr k v (i, cs, kvs)
 stringify :: [Inline] -> Text
 stringify = T.concat . map go
   where
-    go (Str t)         = t
+    go (Str t)            = t
-    go Space           = " "
+    go Space              = " "
-    go SoftBreak       = " "
+    go SoftBreak          = " "
-    go LineBreak       = " "
+    go LineBreak          = " "
-    go (Emph ils)      = stringify ils
+    go (Emph ils)         = stringify ils
-    go (Strong ils)    = stringify ils
+    go (Strong ils)       = stringify ils
-    go (Code _ t)      = t
+    go (Strikeout ils)    = stringify ils
-    go (Link _ ils _)  = stringify ils
+    go (Superscript ils)  = stringify ils
-    go (Image _ ils _) = stringify ils
+    go (Subscript ils)    = stringify ils
-    go (Span _ ils)    = stringify ils
+    go (SmallCaps ils)    = stringify ils
-    go _               = ""
+    go (Underline ils)    = stringify ils
+    go (Quoted _ ils)     = stringify ils
+    go (Cite _ ils)       = stringify ils
+    go (Code _ t)         = t
+    go (Math _ t)         = t
+    go (RawInline _ _)    = ""
+    go (Link _ ils _)     = stringify ils
+    go (Image _ ils _)    = stringify ils
+    go (Span _ ils)       = stringify ils
+    go (Note _)           = ""
 
 -- | HTML-escape a text value for use in attribute values.
+--   Defers to the canonical 'Utils.escapeHtmlText'.
 esc :: Text -> Text
-esc = T.concatMap escChar
+esc = U.escapeHtmlText
-  where
-    escChar '&'  = "&amp;"
-    escChar '<'  = "&lt;"
-    escChar '>'  = "&gt;"
-    escChar '"'  = "&quot;"
-    escChar c    = T.singleton c

build/Filters/Links.hs

@@ -25,14 +25,20 @@ apply = walk classifyLink . walk classifyPdfLink
 --   Preserves the original path in @data-pdf-src@ so the popup thumbnail
 --   provider can locate the corresponding @.thumb.png@ file.
 --   Skips links that are already pointing at the viewer (idempotent).
+--
+--   Handles fragment identifiers (e.g. @/papers/foo.pdf#page=5@): the
+--   fragment is stripped before the @.pdf@ suffix check and re-attached
+--   after the viewer URL so PDF.js's anchor handling works.
 classifyPdfLink :: Inline -> Inline
 classifyPdfLink (Link (ident, classes, kvs) ils (url, title))
     | "/" `T.isPrefixOf` url
-    , ".pdf" `T.isSuffixOf` T.toLower url
+    , let (path, fragment) = T.break (== '#') url
+    , ".pdf" `T.isSuffixOf` T.toLower path
     , "pdf-link" `notElem` classes =
-        let viewerUrl = "/pdfjs/web/viewer.html?file=" <> encodeQueryValue url
+        let viewerUrl = "/pdfjs/web/viewer.html?file="
+                        <> encodeQueryValue path <> fragment
             classes'  = classes ++ ["pdf-link"]
-            kvs'      = kvs ++ [("data-pdf-src", url)]
+            kvs'      = kvs ++ [("data-pdf-src", path)]
         in  Link (ident, classes', kvs') ils (viewerUrl, title)
 classifyPdfLink x = x
 
@@ -53,10 +59,33 @@ classifyLink x = x
 -- Helpers
 -- ---------------------------------------------------------------------------
 
+-- | True if the URL points outside the site's domain.
+--
+--   Uses a strict hostname comparison rather than substring matching, so
+--   that a hostile lookalike like @evil-levineuwirth.org.attacker.com@ is
+--   correctly classified as external (and gets @rel=noopener noreferrer@
+--   plus @target=_blank@ applied).
 isExternal :: Text -> Bool
 isExternal url =
-    ("http://"  `T.isPrefixOf` url || "https://" `T.isPrefixOf` url)
+    case extractHost url of
-    && not ("levineuwirth.org" `T.isInfixOf` url)
+        Nothing   -> False
+        Just host ->
+            not (host == siteHost || ("." <> siteHost) `T.isSuffixOf` host)
+  where
+    siteHost = "levineuwirth.org"
+
+-- | Extract the lowercased hostname from an absolute http(s) URL.
+--   Returns 'Nothing' for non-http(s) URLs (relative paths, mailto:, etc.).
+extractHost :: Text -> Maybe Text
+extractHost url
+    | Just rest <- T.stripPrefix "https://" url = Just (hostOf rest)
+    | Just rest <- T.stripPrefix "http://"  url = Just (hostOf rest)
+    | otherwise                                  = Nothing
+  where
+    hostOf rest =
+        let withPort = T.takeWhile (\c -> c /= '/' && c /= '?' && c /= '#') rest
+            host     = T.takeWhile (/= ':') withPort
+        in  T.toLower host
 
 -- | Icon name for the link, matching a file in /images/link-icons/<name>.svg.
 domainIcon :: Text -> Text

build/Filters/Score.hs

@@ -14,12 +14,16 @@
 -- the appropriate exhibit attributes for gallery.js TOC integration.
 module Filters.Score (inlineScores) where
 
+import           Control.Exception      (IOException, try)
 import           Data.Maybe             (listToMaybe)
 import qualified Data.Text              as T
 import qualified Data.Text.IO           as TIO
+import           System.Directory       (doesFileExist)
 import           System.FilePath        ((</>))
+import           System.IO              (hPutStrLn, stderr)
 import           Text.Pandoc.Definition
 import           Text.Pandoc.Walk       (walkM)
+import qualified Utils                  as U
 
 -- | Walk the Pandoc AST and inline all score-fragment divs.
 --   @baseDir@ is the directory of the source file; image paths in the
@@ -37,11 +41,40 @@ inlineScore baseDir (Div (_, cls, attrs) blocks)
             Nothing   -> return $ Div ("", cls, attrs) blocks
             Just path -> do
                 let fullPath = baseDir </> T.unpack path
-                svgRaw <- TIO.readFile fullPath
+                exists <- doesFileExist fullPath
-                let html = buildHtml mName mCaption (processColors svgRaw)
+                if not exists
-                return $ RawBlock (Format "html") html
+                    then do
+                        hPutStrLn stderr $
+                            "[Score] missing SVG: " ++ fullPath
+                            ++ " (referenced from a score-fragment in " ++ baseDir ++ ")"
+                        return (errorBlock mName ("Missing score: " <> path))
+                    else do
+                        result <- try (TIO.readFile fullPath) :: IO (Either IOException T.Text)
+                        case result of
+                            Left e -> do
+                                hPutStrLn stderr $
+                                    "[Score] read error on " ++ fullPath ++ ": " ++ show e
+                                return (errorBlock mName ("Could not read score: " <> path))
+                            Right svgRaw -> do
+                                let html = buildHtml mName mCaption (processColors svgRaw)
+                                return $ RawBlock (Format "html") html
 inlineScore _ block = return block
 
+-- | Render an inline error block in place of a missing or unreadable score.
+--   Mirrors the convention in 'Filters.Viz.errorBlock' so build failures are
+--   visible to the author without aborting the entire site build.
+errorBlock :: Maybe T.Text -> T.Text -> Block
+errorBlock mName message =
+    RawBlock (Format "html") $ T.concat
+        [ "<figure class=\"score-fragment score-fragment--error\""
+        , maybe "" (\n -> " data-exhibit-name=\"" <> escHtml n <> "\"") mName
+        , ">"
+        , "<div class=\"score-fragment-error\">"
+        , escHtml message
+        , "</div>"
+        , "</figure>"
+        ]
+
 -- | Extract the image src from the first Para that contains an Image inline.
 findImagePath :: [Block] -> Maybe T.Text
 findImagePath blocks = listToMaybe
@@ -86,7 +119,4 @@ buildHtml mName mCaption svgContent = T.concat
     ]
 
 escHtml :: T.Text -> T.Text
-escHtml = T.replace "\"" "&quot;"
+escHtml = U.escapeHtmlText
-        . T.replace ">"  "&gt;"
-        . T.replace "<"  "&lt;"
-        . T.replace "&"  "&amp;"

build/Filters/Sidenotes.hs

@@ -33,13 +33,24 @@ convertNote (Note blocks) = do
     return $ RawInline "html" (renderNote n blocks)
 convertNote x = return x
 
--- | Convert a 1-based counter to a letter label: 1→a, 2→b, … 26→z.
+-- | Convert a 1-based counter to a letter label using base-26 expansion
+--   (Excel-column style): 1→a, 2→b, … 26→z, 27→aa, 28→ab, … 52→az,
+--   53→ba, … 702→zz, 703→aaa.  Guarantees a unique label per counter so
+--   no two sidenotes in a single document collide on @id="sn-…"@.
 toLabel :: Int -> Text
-toLabel n = T.singleton (toEnum (fromEnum 'a' + (n - 1) `mod` 26))
+toLabel n
+    | n <= 0    = "?"
+    | otherwise = T.pack (go n)
+  where
+    go k
+        | k <= 0    = ""
+        | otherwise =
+            let (q, r) = (k - 1) `divMod` 26
+            in go q ++ [toEnum (fromEnum 'a' + r)]
 
 renderNote :: Int -> [Block] -> Text
 renderNote n blocks =
-    let inner = replacePTags (blocksToHtml blocks)
+    let inner = blocksToInlineHtml blocks
         lbl   = toLabel n
     in T.concat
         [ "<sup class=\"sidenote-ref\" id=\"snref-", lbl, "\">"
@@ -51,13 +62,34 @@ renderNote n blocks =
         , "</span>"
         ]
 
--- | Replace <p> / </p> with inline-block spans so that sidenote content
+-- | Render a list of Pandoc blocks for inclusion inside an inline @<span
---   stays valid inside the outer <span class="sidenote">.  A bare <p> inside
+--   class="sidenote">@.  Each top-level @Para@ is wrapped in a
---   a <span> is invalid HTML and causes browsers to implicitly close the span.
+--   @<span class="sidenote-para">@ instead of a @<p>@ (which would be
-replacePTags :: Text -> Text
+--   invalid inside a @<span>@); other block types are rendered with the
-replacePTags =
+--   regular Pandoc HTML writer.
-    T.replace "<p>" "<span class=\"sidenote-para\">"
+--
-    . T.replace "</p>" "</span>"
+--   Operating on the AST is preferred over post-rendered string
+--   substitution because the latter mangles content that legitimately
+--   contains the literal text @<p>@ (e.g. code samples discussing HTML).
+blocksToInlineHtml :: [Block] -> Text
+blocksToInlineHtml = T.concat . map renderOne
+  where
+    renderOne :: Block -> Text
+    renderOne (Para inlines) =
+        "<span class=\"sidenote-para\">"
+        <> inlinesToHtml inlines
+        <> "</span>"
+    renderOne (Plain inlines) =
+        inlinesToHtml inlines
+    renderOne b =
+        blocksToHtml [b]
+
+-- | Render a list of inlines to HTML (no surrounding @<p>@).
+inlinesToHtml :: [Inline] -> Text
+inlinesToHtml inlines =
+    case runPure (writeHtml5String (def :: WriterOptions) (Pandoc mempty [Plain inlines])) of
+        Left  _ -> T.empty
+        Right t -> t
 
 -- | Render a list of Pandoc blocks to an HTML fragment via a pure writer run.
 blocksToHtml :: [Block] -> Text

build/Filters/Smallcaps.hs

@@ -22,6 +22,7 @@ import           Data.Text             (Text)
 import qualified Data.Text             as T
 import           Text.Pandoc.Definition
 import           Text.Pandoc.Walk      (walk)
+import qualified Utils                 as U
 
 -- | Apply smallcaps detection to paragraph-level content.
 --   Skips heading blocks to avoid false positives.
@@ -62,10 +63,4 @@ isAbbreviation t =
     && T.any isAlpha t
 
 escHtml :: Text -> Text
-escHtml = T.concatMap esc
+escHtml = U.escapeHtmlText
-  where
-    esc '<'  = "&lt;"
-    esc '>'  = "&gt;"
-    esc '&'  = "&amp;"
-    esc '"'  = "&quot;"
-    esc c    = T.singleton c

build/Filters/Transclusion.hs

@@ -14,6 +14,7 @@
 module Filters.Transclusion (preprocess) where
 
 import Data.List (isSuffixOf, isPrefixOf, stripPrefix)
+import qualified Utils as U
 
 -- | Apply transclusion substitution to the raw Markdown source string.
 preprocess :: String -> String
@@ -21,14 +22,18 @@ preprocess = unlines . map processLine . lines
 
 processLine :: String -> String
 processLine line =
-    case parseDirective (trim line) of
+    case parseDirective (U.trim line) of
         Nothing             -> line
         Just (url, secAttr) ->
-            "<div class=\"transclude\" data-src=\"" ++ url ++ "\""
+            "<div class=\"transclude\" data-src=\"" ++ escAttr url ++ "\""
             ++ secAttr ++ "></div>"
 
 -- | Parse a {{slug}} or {{slug#section}} directive.
 --   Returns (absolute-url, section-attribute-string) or Nothing.
+--
+--   The section name is HTML-escaped before being interpolated into the
+--   @data-section@ attribute, so a stray @\"@, @&@, @<@, or @>@ in a
+--   section name cannot break the surrounding markup.
 parseDirective :: String -> Maybe (String, String)
 parseDirective s = do
     inner <- stripPrefix "{{" s >>= stripSuffix "}}"
@@ -38,15 +43,29 @@ parseDirective s = do
         (slug, '#' : sec)
             | null sec     -> Just (slugToUrl slug, "")
             | otherwise    -> Just (slugToUrl slug,
-                                    " data-section=\"" ++ sec ++ "\"")
+                                    " data-section=\"" ++ escAttr sec ++ "\"")
         _                  -> Nothing
 
 -- | Convert a slug (possibly with leading slash, possibly with path segments)
---   to a root-relative .html URL.
+--   to a root-relative .html URL.  Idempotent for slugs that already end in
+--   @.html@ so callers can safely pass either form.
 slugToUrl :: String -> String
 slugToUrl slug
-    | "/" `isPrefixOf` slug = slug ++ ".html"
+    | ".html" `isSuffixOf` slug, "/" `isPrefixOf` slug = slug
-    | otherwise              = "/" ++ slug ++ ".html"
+    | ".html" `isSuffixOf` slug                        = "/" ++ slug
+    | "/" `isPrefixOf` slug                            = slug ++ ".html"
+    | otherwise                                        = "/" ++ slug ++ ".html"
+
+-- | Minimal HTML attribute-value escape.
+escAttr :: String -> String
+escAttr = concatMap esc
+  where
+    esc '&'  = "&amp;"
+    esc '<'  = "&lt;"
+    esc '>'  = "&gt;"
+    esc '"'  = "&quot;"
+    esc '\'' = "&#39;"
+    esc c    = [c]
 
 -- | Strip a suffix from a string, returning Nothing if not present.
 stripSuffix :: String -> String -> Maybe String
@@ -54,7 +73,3 @@ stripSuffix suf str
     | suf `isSuffixOf` str = Just (take (length str - length suf) str)
     | otherwise             = Nothing
 
--- | Strip leading and trailing spaces.
-trim :: String -> String
-trim = f . f
-  where f = reverse . dropWhile (== ' ')

build/Filters/Typography.hs

@@ -9,9 +9,9 @@
 module Filters.Typography (apply) where
 
 import           Data.Text    (Text)
-import qualified Data.Text    as T
 import           Text.Pandoc.Definition
 import           Text.Pandoc.Walk (walk)
+import           Utils            (escapeHtmlText)
 
 -- | Apply all typographic transformations to the document.
 apply :: Pandoc -> Pandoc
@@ -38,21 +38,17 @@ abbrevMap =
 
 -- | If the Str token exactly matches a known abbreviation, replace it with
 --   a @RawInline "html"@ @<abbr>@ element; otherwise leave it unchanged.
+--
+--   Both the @title@ attribute and the visible body pass through
+--   'escapeHtmlText' for consistency with every other raw-HTML emitter
+--   in the filter pipeline. The abbreviations themselves are ASCII-safe
+--   so this is defense-in-depth rather than a live hazard.
 expandAbbrev :: Inline -> Inline
 expandAbbrev (Str t) =
     case lookup t abbrevMap of
         Just title ->
             RawInline "html" $
-                "<abbr title=\"" <> title <> "\">" <> escHtml t <> "</abbr>"
+                "<abbr title=\"" <> escapeHtmlText title <> "\">"
+                    <> escapeHtmlText t <> "</abbr>"
         Nothing -> Str t
 expandAbbrev x = x
-
--- | Minimal HTML escaping for the abbr content (should be plain text).
-escHtml :: Text -> Text
-escHtml = T.concatMap esc
-  where
-    esc '<'  = "&lt;"
-    esc '>'  = "&gt;"
-    esc '&'  = "&amp;"
-    esc '"'  = "&quot;"
-    esc c    = T.singleton c

build/Filters/Viz.hs

@@ -39,11 +39,14 @@ module Filters.Viz (inlineViz) where
 import           Control.Exception      (IOException, catch)
 import           Data.Maybe             (fromMaybe)
 import qualified Data.Text              as T
+import           System.Directory       (doesFileExist)
 import           System.Exit            (ExitCode (..))
 import           System.FilePath        ((</>))
+import           System.IO              (hPutStrLn, stderr)
 import           System.Process         (readProcessWithExitCode)
 import           Text.Pandoc.Definition
 import           Text.Pandoc.Walk       (walkM)
+import qualified Utils                  as U
 
 -- ---------------------------------------------------------------------------
 -- Public entry point
@@ -87,19 +90,26 @@ transformBlock _ b = return b
 -- ---------------------------------------------------------------------------
 
 -- | Run @python3 <script>@.  Returns the script\'s stdout on success, or an
---   error message on failure (non-zero exit or missing @script=@ attribute).
+--   error message on failure (non-zero exit, missing @script=@ attribute, or
+--   missing script file).
 runScript :: FilePath -> [(T.Text, T.Text)] -> IO (Either String T.Text)
 runScript baseDir attrs =
     case lookup "script" attrs of
         Nothing -> return (Left "missing script= attribute")
         Just p  -> do
             let fullPath = baseDir </> T.unpack p
-            (ec, out, err) <-
+            exists <- doesFileExist fullPath
-                readProcessWithExitCode "python3" [fullPath] ""
+            if not exists
-                `catch` (\e -> return (ExitFailure 1, "", show (e :: IOException)))
+                then return (Left ("script not found: " ++ fullPath))
-            return $ case ec of
+                else do
-                ExitSuccess   -> Right (T.pack out)
+                    (ec, out, err) <-
-                ExitFailure _ -> Left (if null err then "non-zero exit" else err)
+                        readProcessWithExitCode "python3" [fullPath] ""
+                        `catch` (\e -> return (ExitFailure 1, "", show (e :: IOException)))
+                    return $ case ec of
+                        ExitSuccess   -> Right (T.pack out)
+                        ExitFailure _ -> Left $
+                            "in " ++ fullPath ++ ": "
+                            ++ (if null err then "non-zero exit" else err)
 
 -- ---------------------------------------------------------------------------
 -- SVG colour post-processing (mirrors Filters.Score.processColors)
@@ -173,10 +183,7 @@ attr :: T.Text -> [(T.Text, T.Text)] -> T.Text
 attr key kvs = fromMaybe "" (lookup key kvs)
 
 warn :: String -> String -> IO ()
-warn kind msg = putStrLn $ "[Viz] " ++ kind ++ " error: " ++ msg
+warn kind msg = hPutStrLn stderr $ "[Viz] " ++ kind ++ " error: " ++ msg
 
 escHtml :: T.Text -> T.Text
-escHtml = T.replace "&"  "&amp;"
+escHtml = U.escapeHtmlText
-        . T.replace "<"  "&lt;"
-        . T.replace ">"  "&gt;"
-        . T.replace "\"" "&quot;"

build/Filters/Wikilinks.hs

@@ -15,6 +15,7 @@ module Filters.Wikilinks (preprocess) where
 
 import           Data.Char    (isAlphaNum, toLower, isSpace)
 import           Data.List    (intercalate)
+import qualified Utils        as U
 
 -- | Scan the raw Markdown source for @[[…]]@ wikilinks and replace them
 --   with standard Markdown link syntax.
@@ -29,21 +30,49 @@ preprocess ('[':'[':rest) =
 preprocess (c:rest) = c : preprocess rest
 
 -- | Convert the inner content of @[[…]]@ to a Markdown link.
+--
+--   Display text is escaped via 'escMdLinkText' so that a literal @]@, @[@,
+--   or backslash in the display does not break the surrounding Markdown
+--   link syntax. The URL itself is produced by 'slugify' and therefore only
+--   ever contains @[a-z0-9-]@, so no URL-side encoding is needed — adding
+--   one would be defense against a character set we can't produce.
 toMarkdownLink :: String -> String
 toMarkdownLink inner =
     let (title, display) = splitOnPipe inner
         url              = "/" ++ slugify title
-    in "[" ++ display ++ "](" ++ url ++ ")"
+    in "[" ++ escMdLinkText display ++ "](" ++ url ++ ")"
+
+-- | Escape the minimum set of characters that would prematurely terminate
+--   a Markdown link's display-text segment: backslash (escape char), @[@,
+--   and @]@. Backslash MUST be escaped first so the escapes we introduce
+--   for @[@ and @]@ are not themselves re-escaped.
+--
+--   Deliberately NOT escaped: @_@, @*@, @\`@, @<@. Those are inline
+--   formatting markers in Markdown and escaping them would strip the
+--   author's ability to put emphasis, code, or inline HTML in a wikilink's
+--   display text.
+escMdLinkText :: String -> String
+escMdLinkText = concatMap esc
+  where
+    esc '\\' = "\\\\"
+    esc '['  = "\\["
+    esc ']'  = "\\]"
+    esc c    = [c]
 
 -- | Split on the first @|@; if none, display = title.
 splitOnPipe :: String -> (String, String)
 splitOnPipe s =
     case break (== '|') s of
-        (title, '|':display) -> (trim title, trim display)
+        (title, '|':display) -> (U.trim title, U.trim display)
-        _                    -> (trim s,     trim s)
+        _                    -> (U.trim s,     U.trim s)
 
 -- | Produce a URL slug: lowercase, words joined by hyphens,
 --   non-alphanumeric characters removed.
+--
+--   Trailing punctuation is dropped rather than preserved as a dangling
+--   hyphen — @slugify "end." == "end"@, not @"end-"@. This is intentional:
+--   author-authored wikilinks tend to end sentences with a period and the
+--   desired URL is almost always the terminal-punctuation-free form.
 slugify :: String -> String
 slugify = intercalate "-" . words . map toLowerAlnum
   where
@@ -55,5 +84,3 @@ slugify = intercalate "-" . words . map toLowerAlnum
                                 -- split correctly and double-hyphens are
                                 -- collapsed by 'words'
 
-trim :: String -> String
-trim = reverse . dropWhile (== ' ') . reverse . dropWhile (== ' ')

build/Metadata.hs

@@ -1,2 +0,0 @@
--- | Metadata utilities (Phase 2+).
-module Metadata where

build/Patterns.hs

@@ -0,0 +1,100 @@
+{-# LANGUAGE GHC2021 #-}
+{-# LANGUAGE OverloadedStrings #-}
+-- | Canonical content-pattern definitions, shared across modules.
+--
+-- Several modules need to enumerate "all author-written content" or
+-- "all essays". Historically each module hard-coded its own slightly
+-- different list, which produced silent omissions (e.g. directory-form
+-- essays not appearing on author pages). This module is the single source
+-- of truth — every place that needs a content pattern should import from
+-- here, not write its own.
+module Patterns
+    ( -- * Per-section patterns
+      essayPattern
+    , draftEssayPattern
+    , blogPattern
+    , poetryPattern
+    , fictionPattern
+    , musicPattern
+    , standalonePagesPattern
+      -- * Aggregated patterns
+    , allWritings        -- essays + blog + poetry + fiction
+    , allContent         -- everything that backlinks should index
+    , authorIndexable    -- everything that should appear on /authors/{slug}/
+    , tagIndexable       -- everything that should appear on /<tag>/
+    ) where
+
+import Hakyll
+
+-- ---------------------------------------------------------------------------
+-- Per-section
+-- ---------------------------------------------------------------------------
+
+-- | All published essays — flat files and directory-based (with co-located
+-- assets). Drafts under @content/drafts/essays/**@ are intentionally NOT
+-- included; 'Site.rules' unions them in conditionally when @SITE_ENV=dev@.
+essayPattern :: Pattern
+essayPattern = "content/essays/*.md" .||. "content/essays/*/index.md"
+
+-- | In-progress essay drafts. Matches the flat and directory forms under
+-- @content/drafts/essays/@. Only 'Site.rules' consumes this, gated on
+-- @SITE_ENV=dev@ — every other module that enumerates content (Authors,
+-- Tags, Backlinks, Stats, feeds) sees only 'essayPattern', so drafts are
+-- automatically invisible to listings, tags, authors, backlinks, and stats.
+draftEssayPattern :: Pattern
+draftEssayPattern =
+       "content/drafts/essays/*.md"
+  .||. "content/drafts/essays/*/index.md"
+
+-- | All blog posts.  Currently flat-only; co-located blog assets would
+-- require a directory variant analogous to 'essayPattern'.
+blogPattern :: Pattern
+blogPattern = "content/blog/*.md"
+
+-- | All poetry: flat poems plus collection poems, excluding collection
+-- index pages (which are landing pages, not poems).
+poetryPattern :: Pattern
+poetryPattern =
+       "content/poetry/*.md"
+  .||. ("content/poetry/*/*.md" .&&. complement "content/poetry/*/index.md")
+
+-- | All fiction. Currently flat-only.
+fictionPattern :: Pattern
+fictionPattern = "content/fiction/*.md"
+
+-- | Music compositions (landing pages live at @content/music/<slug>/index.md@).
+musicPattern :: Pattern
+musicPattern = "content/music/*/index.md"
+
+-- | Top-level standalone pages (about, colophon, current, gpg, …).
+standalonePagesPattern :: Pattern
+standalonePagesPattern = "content/*.md"
+
+-- ---------------------------------------------------------------------------
+-- Aggregations
+-- ---------------------------------------------------------------------------
+
+-- | All long-form authored writings.
+allWritings :: Pattern
+allWritings = essayPattern .||. blogPattern .||. poetryPattern .||. fictionPattern
+
+-- | Every content file the backlinks pass should index. Includes music
+-- landing pages and top-level standalone pages, in addition to writings.
+allContent :: Pattern
+allContent =
+       essayPattern
+  .||. blogPattern
+  .||. poetryPattern
+  .||. fictionPattern
+  .||. musicPattern
+  .||. standalonePagesPattern
+
+-- | Content shown on author index pages — essays + blog posts.
+-- (Poetry and fiction have their own dedicated indexes and are not
+-- aggregated by author.)
+authorIndexable :: Pattern
+authorIndexable = (essayPattern .||. blogPattern) .&&. hasNoVersion
+
+-- | Content shown on tag index pages — essays + blog posts.
+tagIndexable :: Pattern
+tagIndexable = (essayPattern .||. blogPattern) .&&. hasNoVersion

build/SimilarLinks.hs

@@ -18,10 +18,12 @@
 module SimilarLinks (similarLinksField) where
 
 import           Data.Maybe                 (fromMaybe)
+import qualified Data.ByteString            as BS
 import qualified Data.Map.Strict            as Map
 import           Data.Map.Strict            (Map)
 import qualified Data.Text                  as T
 import qualified Data.Text.Encoding         as TE
+import qualified Data.Text.Encoding.Error   as TE
 import qualified Data.Aeson                 as Aeson
 import           Hakyll
 
@@ -83,7 +85,29 @@ normaliseUrl url =
         t3 = fromMaybe t2 (T.stripSuffix "index.html" t2)
         -- strip bare .html extension only for non-index pages
         t4 = fromMaybe t3 (T.stripSuffix ".html" t3)
-    in  T.unpack t4
+    in  percentDecode (T.unpack t4)
+
+-- | Percent-decode @%XX@ escapes (UTF-8) so percent-encoded paths
+-- collide with their decoded form on map lookup. Mirrors
+-- 'Backlinks.percentDecode'; the two implementations are intentionally
+-- duplicated because they apply different normalisations *before*
+-- decoding (Backlinks strips @.html@ unconditionally; SimilarLinks
+-- preserves the trailing-slash form for index pages).
+percentDecode :: String -> String
+percentDecode = T.unpack . TE.decodeUtf8With TE.lenientDecode . BS.pack . go
+  where
+    go []                 = []
+    go ('%':a:b:rest)
+        | Just hi <- hexDigit a
+        , Just lo <- hexDigit b
+        = fromIntegral (hi * 16 + lo) : go rest
+    go (c:rest)           = fromIntegral (fromEnum c) : go rest
+
+    hexDigit c
+        | c >= '0' && c <= '9' = Just (fromEnum c - fromEnum '0')
+        | c >= 'a' && c <= 'f' = Just (fromEnum c - fromEnum 'a' + 10)
+        | c >= 'A' && c <= 'F' = Just (fromEnum c - fromEnum 'A' + 10)
+        | otherwise            = Nothing
 
 -- ---------------------------------------------------------------------------
 -- HTML rendering

build/Site.hs

@@ -2,10 +2,13 @@
 {-# LANGUAGE OverloadedStrings #-}
 module Site (rules) where
 
-import Control.Monad (filterM)
+import Control.Monad (filterM, when)
-import Data.List     (intercalate, isPrefixOf)
+import Data.List     (isPrefixOf)
 import Data.Maybe    (fromMaybe)
+import System.Environment (lookupEnv)
 import System.FilePath (takeDirectory, takeFileName, replaceExtension)
+import qualified Data.Aeson as Aeson
+import qualified Data.ByteString.Lazy.Char8 as LBS
 import Hakyll
 import Authors    (buildAllAuthors, applyAuthorRules)
 import Backlinks  (backlinkRules)
@@ -15,14 +18,11 @@ import Catalog      (musicCatalogCtx)
 import Commonplace  (commonplaceCtx)
 import Contexts   (siteCtx, essayCtx, postCtx, pageCtx, poetryCtx, fictionCtx, compositionCtx,
                    contentKindField)
+import qualified Patterns as P
 import Tags       (buildAllTags, applyTagRules)
 import Pagination (blogPaginateRules)
 import Stats      (statsRules)
 
--- All essays: flat files and directory-based (with co-located assets).
-allEssays :: Pattern
-allEssays = "content/essays/*.md" .||. "content/essays/*/index.md"
-
 -- Poems inside collection subdirectories, excluding their index pages.
 collectionPoems :: Pattern
 collectionPoems = "content/poetry/*/*.md" .&&. complement "content/poetry/*/index.md"
@@ -51,6 +51,16 @@ musicFeedConfig = FeedConfiguration
 
 rules :: Rules ()
 rules = do
+    -- ---------------------------------------------------------------------------
+    -- Build mode. SITE_ENV=dev (set by `make dev` / `make watch`) includes
+    -- drafts under content/drafts/**; anything else (unset, "deploy", "build")
+    -- excludes them entirely from every match, listing, and asset rule below.
+    -- ---------------------------------------------------------------------------
+    isDev <- preprocess $ (== Just "dev") <$> lookupEnv "SITE_ENV"
+    let allEssays = if isDev
+                    then P.essayPattern .||. P.draftEssayPattern
+                    else P.essayPattern
+
     -- ---------------------------------------------------------------------------
     -- Backlinks (pass 1: link extraction; pass 2: JSON generation)
     -- Must run before content rules so dependencies resolve correctly.
@@ -70,8 +80,14 @@ rules = do
     applyTagRules tags siteCtx
     statsRules tags
 
-    -- Per-page JS files — authored alongside content in content/**/*.js
+    -- Per-page JS files — authored alongside content in content/**/*.js.
-    match "content/**/*.js" $ do
+    -- Draft JS is handled by a separate dev-only rule below.
+    match ("content/**/*.js" .&&. complement "content/drafts/**") $ do
+        route   $ gsubRoute "content/" (const "")
+        compile copyFileCompiler
+
+    -- Per-page JS co-located with draft essays (dev-only).
+    when isDev $ match "content/drafts/**/*.js" $ do
         route   $ gsubRoute "content/" (const "")
         compile copyFileCompiler
 
@@ -177,14 +193,25 @@ rules = do
 
     -- ---------------------------------------------------------------------------
     -- Essays — flat (content/essays/foo.md → essays/foo.html) and
-    --          directory-based (content/essays/slug/index.md → essays/slug/index.html)
+    --          directory-based (content/essays/slug/index.md → essays/slug/index.html).
+    --          In dev mode, drafts under content/drafts/essays/ route to
+    --          drafts/essays/foo.html (flat) or drafts/essays/slug/index.html (dir).
     -- ---------------------------------------------------------------------------
     match allEssays $ do
         route $ customRoute $ \ident ->
-            let fp = toFilePath ident
+            let fp       = toFilePath ident
-            in if takeFileName fp == "index.md"
+                fname    = takeFileName fp
-               then replaceExtension (drop 8 fp) "html"
+                isIndex  = fname == "index.md"
-               else "essays/" ++ replaceExtension (takeFileName fp) "html"
+                isDraft  = "content/drafts/essays/" `isPrefixOf` fp
+            in case (isDraft, isIndex) of
+                -- content/drafts/essays/slug/index.md → drafts/essays/slug/index.html
+                (True,  True)  -> replaceExtension (drop 8 fp) "html"
+                -- content/drafts/essays/foo.md        → drafts/essays/foo.html
+                (True,  False) -> "drafts/essays/" ++ replaceExtension fname "html"
+                -- content/essays/slug/index.md        → essays/slug/index.html
+                (False, True)  -> replaceExtension (drop 8 fp) "html"
+                -- content/essays/foo.md               → essays/foo.html
+                (False, False) -> "essays/" ++ replaceExtension fname "html"
         compile $ essayCompiler
             >>= saveSnapshot "content"
             >>= loadAndApplyTemplate "templates/essay.html"   essayCtx
@@ -198,6 +225,13 @@ rules = do
         route $ gsubRoute "content/" (const "")
         compile copyFileCompiler
 
+    -- Static assets co-located with draft essays (dev-only).
+    when isDev $ match ("content/drafts/essays/**"
+                        .&&. complement "content/drafts/essays/*.md"
+                        .&&. complement "content/drafts/essays/*/index.md") $ do
+        route $ gsubRoute "content/" (const "")
+        compile copyFileCompiler
+
     -- ---------------------------------------------------------------------------
     -- Blog posts
     -- ---------------------------------------------------------------------------
@@ -400,7 +434,7 @@ rules = do
             poetry  <- loadAll ("content/poetry/*.md"  .&&. hasNoVersion) :: Compiler [Item String]
             routes  <- mapM (getRoute . itemIdentifier) (essays ++ posts ++ fiction ++ poetry)
             let urls = [ "/" ++ r | Just r <- routes ]
-            makeItem $ "[" ++ intercalate "," (map show urls) ++ "]"
+            makeItem $ LBS.unpack (Aeson.encode urls)
 
     -- ---------------------------------------------------------------------------
     -- Atom feed — all content sorted by date

build/Stability.hs

@@ -29,7 +29,9 @@ import Data.Maybe               (catMaybes, fromMaybe, listToMaybe)
 import Data.Time.Calendar       (Day, diffDays)
 import Data.Time.Format         (parseTimeM, formatTime, defaultTimeLocale)
 import qualified Data.Text      as T
+import qualified Data.Text.IO   as TIO
 import System.Exit              (ExitCode (..))
+import System.IO                (hPutStrLn, stderr)
 import System.Process           (readProcessWithExitCode)
 import Hakyll
 
@@ -39,9 +41,12 @@ import Hakyll
 
 -- | Read @IGNORE.txt@ (paths relative to project root, one per line).
 -- Returns an empty list when the file is absent or empty.
+--
+-- Uses strict text IO so the file handle is released immediately rather
+-- than left dangling on the lazy spine of 'readFile'.
 readIgnore :: IO [FilePath]
 readIgnore =
-    (filter (not . null) . lines <$> readFile "IGNORE.txt")
+    (filter (not . null) . map T.unpack . T.lines <$> TIO.readFile "IGNORE.txt")
     `catch` \(_ :: IOException) -> return []
 
 -- ---------------------------------------------------------------------------
@@ -49,13 +54,24 @@ readIgnore =
 -- ---------------------------------------------------------------------------
 
 -- | Return commit dates (ISO "YYYY-MM-DD", newest-first) for @fp@.
+--
+-- Logs git's stderr to the build's stderr when present so the author
+-- isn't left in the dark when a file isn't tracked yet (the warning
+-- otherwise vanishes silently).
 gitDates :: FilePath -> IO [String]
 gitDates fp = do
-    (ec, out, _) <- readProcessWithExitCode
+    (ec, out, err) <- readProcessWithExitCode
         "git" ["log", "--follow", "--format=%ad", "--date=short", "--", fp] ""
     case ec of
-        ExitFailure _ -> return []
+        ExitFailure _ -> do
-        ExitSuccess   -> return $ filter (not . null) (lines out)
+            let msg = if null err then "git log failed" else err
+            hPutStrLn stderr $ "[Stability] " ++ fp ++ ": " ++ msg
+            return []
+        ExitSuccess   -> do
+            case err of
+                "" -> return ()
+                _  -> hPutStrLn stderr $ "[Stability] " ++ fp ++ ": " ++ err
+            return $ filter (not . null) (lines out)
 
 -- | Parse an ISO "YYYY-MM-DD" string to a 'Day'.
 parseIso :: String -> Maybe Day
@@ -69,17 +85,38 @@ daySpan oldest newest =
         _                -> 0
 
 -- | Derive stability label from commit dates (newest-first).
+--
+-- Thresholds (commit count + age in days since first commit):
+--
+--   * @volatile@      — solo commit OR less than two weeks old.
+--   * @revising@      — under six commits AND under three months old.
+--   * @fairly stable@ — under sixteen commits OR under one year old.
+--   * @stable@        — under thirty-one commits OR under two years old.
+--   * @established@   — anything beyond.
+--
+-- These cliffs are deliberately conservative: a fast burst of commits
+-- early in a piece's life looks volatile until enough time has passed
+-- to demonstrate it has settled.
 stabilityFromDates :: [String] -> String
 stabilityFromDates [] = "volatile"
-stabilityFromDates dates =
+stabilityFromDates dates@(newest : _) =
-    classify (length dates) (daySpan (last dates) (head dates))
+    let oldest = case reverse dates of
+                    (x : _) -> x
+                    []      -> newest          -- unreachable; matched above
+    in  classify (length dates) (daySpan oldest newest)
   where
     classify n age
-        | n <= 1 || age < 14   = "volatile"
+        | n <= 1 || age < volatileAge        = "volatile"
-        | n <= 5  && age < 90  = "revising"
+        | n <= 5  && age < revisingAge       = "revising"
-        | n <= 15 || age < 365 = "fairly stable"
+        | n <= 15 || age < fairlyStableAge   = "fairly stable"
-        | n <= 30 || age < 730 = "stable"
+        | n <= 30 || age < stableAge         = "stable"
-        | otherwise            = "established"
+        | otherwise                          = "established"
+
+    volatileAge, revisingAge, fairlyStableAge, stableAge :: Int
+    volatileAge     = 14
+    revisingAge     = 90
+    fairlyStableAge = 365
+    stableAge       = 730
 
 -- | Format an ISO date as "%-d %B %Y" (e.g. "16 March 2026").
 fmtIso :: String -> String

build/Stats.hs

@@ -8,15 +8,18 @@ module Stats (statsRules) where
 
 import Control.Exception          (IOException, catch)
 import Control.Monad              (forM)
-import Data.List                  (find, isSuffixOf, sort, sortBy)
+import Data.Char                  (isSpace, toLower)
+import Data.List                  (find, isPrefixOf, isSuffixOf, sort, sortBy)
 import qualified Data.Map.Strict  as Map
 import Data.Maybe                 (catMaybes, fromMaybe, isJust, listToMaybe)
 import Data.Ord                   (comparing, Down (..))
 import qualified Data.Set         as Set
+import Data.String                (fromString)
 import Data.Time                  (getCurrentTime, formatTime, defaultTimeLocale,
                                    Day, parseTimeM, utctDay, addDays, diffDays)
 import Data.Time.Calendar         (toGregorian, dayOfWeek)
-import System.Directory           (doesDirectoryExist, getFileSize, listDirectory)
+import System.Directory           (doesDirectoryExist, getFileSize, listDirectory,
+                                   pathIsSymbolicLink)
 import System.Exit                (ExitCode (..))
 import System.FilePath            (takeExtension, (</>))
 import System.Process             (readProcessWithExitCode)
@@ -26,10 +29,15 @@ import qualified Data.Aeson.Key   as AK
 import qualified Data.Aeson.KeyMap as KM
 import qualified Data.Vector      as V
 import qualified Data.Text        as T
+import qualified Data.Text.IO     as TIO
 import qualified Data.Text.Encoding as TE
+import qualified Text.Blaze.Html5            as H
+import qualified Text.Blaze.Html5.Attributes as A
+import           Text.Blaze.Html.Renderer.String (renderHtml)
+import qualified Text.Blaze.Internal         as BI
 import Hakyll
-import Authors                    (authorLinksField)
+import Contexts                   (siteCtx, authorLinksField)
-import Contexts                   (siteCtx)
+import qualified Patterns         as P
 import Utils                      (readingTime)
 
 -- ---------------------------------------------------------------------------
@@ -100,10 +108,49 @@ pctStr _ 0     = "—"
 pctStr n total = show (n * 100 `div` total) ++ "%"
 
 -- | Strip HTML tags for plain-text word counting.
+--
+-- Handles:
+--   * Tag bodies, including @>@ inside double-quoted attribute values
+--     (so @\<img alt=\"a > b\"\>@ doesn't slice the surrounding text).
+--   * HTML comments @\<!-- ... --\>@ as a unit.
+--   * @\<![CDATA[ ... ]]\>@ sections.
+--
+-- This is still a heuristic — it does not validate the HTML — but it
+-- closes the most common ways for "tag stripping" to leak content.
 stripHtmlTags :: String -> String
-stripHtmlTags []         = []
+stripHtmlTags = go
-stripHtmlTags ('<':rest) = stripHtmlTags (drop 1 (dropWhile (/= '>') rest))
+  where
-stripHtmlTags (c:rest)   = c : stripHtmlTags rest
+    go []                                = []
+    go ('<':'!':'-':'-':rest)            = go (dropComment rest)
+    go ('<':'!':'[':'C':'D':'A':'T':'A':'[':rest)
+                                         = go (dropCdata rest)
+    go ('<':rest)                        = go (dropTag rest)
+    go (c:rest)                          = c : go rest
+
+    -- Drop everything up to and including "-->".
+    dropComment ('-':'-':'>':rs) = rs
+    dropComment (_:rs)           = dropComment rs
+    dropComment []               = []
+
+    -- Drop everything up to and including "]]>".
+    dropCdata (']':']':'>':rs) = rs
+    dropCdata (_:rs)           = dropCdata rs
+    dropCdata []               = []
+
+    -- Drop a tag body, respecting double-quoted attribute values.
+    dropTag ('"':rs)  = dropTag (skipQuoted rs)
+    dropTag ('\'':rs) = dropTag (skipApos   rs)
+    dropTag ('>':rs)  = rs
+    dropTag (_:rs)    = dropTag rs
+    dropTag []        = []
+
+    skipQuoted ('"':rs) = rs
+    skipQuoted (_:rs)   = skipQuoted rs
+    skipQuoted []       = []
+
+    skipApos ('\'':rs) = rs
+    skipApos (_:rs)    = skipApos rs
+    skipApos []        = []
 
 -- | Normalise a page URL for backlink map lookup (strip trailing .html).
 normUrl :: String -> String
@@ -114,10 +161,16 @@ normUrl u
 pad2 :: (Show a, Integral a) => a -> String
 pad2 n = if n < 10 then "0" ++ show n else show n
 
--- | Median of a non-empty list; returns 0 for empty.
+-- | Median of a non-empty list; returns 0 for empty. Uses 'drop' +
+-- pattern match instead of @(!!)@ so the function is total in its
+-- own implementation, not just by external invariant.
 median :: [Int] -> Int
 median [] = 0
-median xs = let s = sort xs in s !! (length s `div` 2)
+median xs =
+    case drop (length xs `div` 2) (sort xs) of
+        (m : _) -> m
+        []      -> 0   -- unreachable: length xs >= 1 above
+
 
 -- ---------------------------------------------------------------------------
 -- Date helpers (for /stats/ page)
@@ -145,83 +198,169 @@ shortMonth m = case m of
     9 -> "Sep"; 10 -> "Oct"; 11 -> "Nov"; 12 -> "Dec"
     _ -> ""
 
+-- ---------------------------------------------------------------------------
+-- URL sanitization and core HTML combinators
+-- ---------------------------------------------------------------------------
+
+-- | Defense-in-depth URL allowlist: reject anything that isn't an internal
+-- path, a fragment, or an explicit safe scheme. Case-insensitive and
+-- whitespace-tolerant to block @JavaScript:@, @\tjavascript:@, @data:@, etc.
+-- @http://@ is intentionally excluded to avoid mixed-content warnings.
+--
+-- Protocol-relative URLs (@//evil.com@) are rejected because the leading
+-- slash would otherwise admit them through the @\"\/\"@ prefix check.
+isSafeUrl :: String -> Bool
+isSafeUrl u =
+    let norm = map toLower (dropWhile isSpace u)
+    in  not ("//" `isPrefixOf` norm)
+        && any (`isPrefixOf` norm) ["/", "https://", "mailto:", "#"]
+
+safeHref :: String -> H.AttributeValue
+safeHref u
+  | isSafeUrl u = H.stringValue u
+  | otherwise   = H.stringValue "#"
+
+-- | Shorthand for 'H.toHtml' over a 'String'.
+txt :: String -> H.Html
+txt = H.toHtml
+
+-- | Anchor element with escaped title text and URL sanitized via 'safeHref'.
+-- Use for trusted plain-text labels such as tag slugs.
+link :: String -> String -> H.Html
+link url title = H.a H.! A.href (safeHref url) $ H.toHtml title
+
+-- | Anchor for a content page, where the title comes from frontmatter and
+-- may contain author-authored inline HTML (e.g. @<em>Book Title</em>@).
+-- The URL is still sanitized via 'safeHref'; the title is emitted
+-- pre-escaped, matching site convention that metadata titles are
+-- author-controlled trusted HTML.
+pageLink :: String -> String -> H.Html
+pageLink url title = H.a H.! A.href (safeHref url) $ H.preEscapedToHtml title
+
+-- | Typed section header followed by its body content.
+section :: String -> String -> H.Html -> H.Html
+section id_ title body = do
+    H.h2 H.! A.id (H.stringValue id_) $ H.toHtml title
+    body
+
+-- | Build-telemetry table with header row, body rows, and an optional total
+-- row. Cell contents are pre-rendered 'H.Html' so callers may embed links or
+-- emphasis inside cells without risking double-escaping.
+table :: [String] -> [[H.Html]] -> Maybe [H.Html] -> H.Html
+table headers rows mFoot =
+    H.table H.! A.class_ "build-table" $ do
+        H.thead $ H.tr $ mapM_ (H.th . H.toHtml) headers
+        H.tbody $ mapM_ renderRow rows
+        maybe (return ()) renderFoot mFoot
+  where
+    renderRow cells  = H.tr $ mapM_ H.td cells
+    renderFoot cells = H.tfoot $
+        H.tr H.! A.class_ "build-total" $ mapM_ H.td cells
+
+-- | Two-column metadata block: each pair becomes a @<dt>/<dd>@ entry. Values
+-- are 'H.Html' to allow mixing links and plain text.
+dl :: [(String, H.Html)] -> H.Html
+dl pairs = H.dl H.! A.class_ "build-meta" $
+    mapM_ (\(k, v) -> do H.dt (H.toHtml k); H.dd v) pairs
+
+-- ---------------------------------------------------------------------------
+-- SVG / custom element helpers (no blaze-svg dependency)
+-- ---------------------------------------------------------------------------
+
+svgTag, rectTag, textTag, titleTag :: H.Html -> H.Html
+svgTag   = BI.customParent "svg"
+rectTag  = BI.customParent "rect"
+textTag  = BI.customParent "text"
+titleTag = BI.customParent "title"
+
+-- | Attach an attribute that isn't in 'Text.Blaze.Html5.Attributes' (e.g.
+-- SVG @viewBox@, @x@, @y@, or @data-target@).
+customAttr :: String -> String -> H.Attribute
+customAttr name val = BI.customAttribute (fromString name) (fromString val)
+
 -- ---------------------------------------------------------------------------
 -- Heatmap SVG
 -- ---------------------------------------------------------------------------
 
--- | 52-week writing activity heatmap (inline SVG, CSS-variable colors).
+-- | 52-week writing activity heatmap. Styled via @.heatmap-svg@ rules in
-renderHeatmap :: Map.Map Day Int -> Day -> String
+-- static/css/build.css (no inline @<style>@).
+renderHeatmap :: Map.Map Day Int -> Day -> H.Html
 renderHeatmap wordsByDay today =
-    let cellSz  = 10 :: Int
+    let cellSz   = 10 :: Int
-        gap     = 2  :: Int
+        gap      = 2  :: Int
-        step    = cellSz + gap
+        step     = cellSz + gap
-        hdrH    = 22 :: Int       -- vertical space for month labels
+        hdrH     = 22 :: Int              -- vertical space for month labels
-        nWeeks  = 52
+        nWeeks   = 52
         -- First Monday of the 52-week window
         startDay = addDays (fromIntegral (-(nWeeks - 1)) * 7) (weekStart today)
         nDays    = diffDays today startDay + 1
         allDays  = [addDays i startDay | i <- [0 .. nDays - 1]]
         weekOf d = fromIntegral (diffDays d startDay `div` 7) :: Int
-        dowOf  d = fromEnum (dayOfWeek d)        -- Mon=0..Sun=6
+        dowOf  d = fromEnum (dayOfWeek d)                 -- Mon=0..Sun=6
         svgW     = (nWeeks - 1) * step + cellSz
         svgH     = 6 * step + cellSz + hdrH
 
-        -- Month labels: one per first-of-month day
+        monthLabel d =
-        monthLbls = concatMap (\d ->
             let (_, mo, da) = toGregorian d
             in  if da == 1
-                then "<text class=\"hm-lbl\" x=\"" ++ show (weekOf d * step)
+                then textTag H.! A.class_ "hm-lbl"
-                  ++ "\" y=\"14\">" ++ shortMonth mo ++ "</text>"
+                             H.! customAttr "x" (show (weekOf d * step))
-                else "") allDays
+                             H.! customAttr "y" "14"
+                           $ txt (shortMonth mo)
+                else mempty
 
-        -- One rect per day
+        dayCell d =
-        cells = concatMap (\d ->
+            let wc           = fromMaybe 0 (Map.lookup d wordsByDay)
-            let wc         = fromMaybe 0 (Map.lookup d wordsByDay)
                 (yr, mo, da) = toGregorian d
-                x          = weekOf d * step
+                x            = weekOf d * step
-                y          = dowOf d * step + hdrH
+                y            = dowOf d * step + hdrH
-                tip        = show yr ++ "-" ++ pad2 mo ++ "-" ++ pad2 da
+                tip          = show yr ++ "-" ++ pad2 mo ++ "-" ++ pad2 da
-                          ++ if wc > 0 then ": " ++ commaInt wc ++ " words" else ""
+                            ++ if wc > 0 then ": " ++ commaInt wc ++ " words" else ""
-            in  "<rect class=\"" ++ heatClass wc ++ "\""
+            in  rectTag H.! A.class_ (H.stringValue (heatClass wc))
-             ++ " x=\"" ++ show x ++ "\" y=\"" ++ show y ++ "\""
+                        H.! customAttr "x"      (show x)
-             ++ " width=\"" ++ show cellSz ++ "\" height=\"" ++ show cellSz ++ "\""
+                        H.! customAttr "y"      (show y)
-             ++ " rx=\"2\"><title>" ++ tip ++ "</title></rect>") allDays
+                        H.! customAttr "width"  (show cellSz)
+                        H.! customAttr "height" (show cellSz)
+                        H.! customAttr "rx"     "2"
+                      $ titleTag (txt tip)
 
-        -- Inline legend (five sample rects)
         legendW = 5 * step - gap
-        legendSvg =
+        legendCell i =
-            "<svg width=\"" ++ show legendW ++ "\" height=\"" ++ show cellSz ++ "\""
+            rectTag H.! A.class_ (H.stringValue ("hm" ++ show i))
-         ++ " viewBox=\"0 0 " ++ show legendW ++ " " ++ show cellSz ++ "\""
+                    H.! customAttr "x"      (show (i * step))
-         ++ " style=\"display:inline;vertical-align:middle\">"
+                    H.! customAttr "y"      "0"
-         ++ concatMap (\i ->
+                    H.! customAttr "width"  (show cellSz)
-                "<rect class=\"hm" ++ show i ++ "\""
+                    H.! customAttr "height" (show cellSz)
-             ++ " x=\"" ++ show (i * step) ++ "\" y=\"0\""
+                    H.! customAttr "rx"     "2"
-             ++ " width=\"" ++ show cellSz ++ "\" height=\"" ++ show cellSz ++ "\""
+                  $ mempty
-             ++ " rx=\"2\"/>") [0..4]
-         ++ "</svg>"
 
-    in  "<figure class=\"stats-heatmap\">"
+        legendSvg =
-     ++ "<svg width=\"" ++ show svgW ++ "\" height=\"" ++ show svgH ++ "\""
+            svgTag H.! customAttr "width"   (show legendW)
-     ++ " viewBox=\"0 0 " ++ show svgW ++ " " ++ show svgH ++ "\""
+                   H.! customAttr "height"  (show cellSz)
-     ++ " class=\"heatmap-svg\" role=\"img\""
+                   H.! customAttr "viewBox" ("0 0 " ++ show legendW ++ " " ++ show cellSz)
-     ++ " aria-label=\"52-week writing activity heatmap\">"
+                   H.! customAttr "style"   "display:inline;vertical-align:middle"
-     ++ "<style>"
+                 $ mapM_ legendCell [0 .. 4 :: Int]
-     ++ ".hm0{fill:var(--hm-0)}.hm1{fill:var(--hm-1)}.hm2{fill:var(--hm-2)}"
+
-     ++ ".hm3{fill:var(--hm-3)}.hm4{fill:var(--hm-4)}"
+    in  H.figure H.! A.class_ "stats-heatmap" $ do
-     ++ ".hm-lbl{font-size:9px;fill:var(--text-faint);font-family:sans-serif}"
+            svgTag H.! customAttr "width"      (show svgW)
-     ++ "</style>"
+                   H.! customAttr "height"     (show svgH)
-     ++ monthLbls ++ cells
+                   H.! customAttr "viewBox"    ("0 0 " ++ show svgW ++ " " ++ show svgH)
-     ++ "</svg>"
+                   H.! A.class_ "heatmap-svg"
-     ++ "<figcaption class=\"heatmap-legend\">"
+                   H.! customAttr "role"       "img"
-     ++ "Less\xA0" ++ legendSvg ++ "\xA0More"
+                   H.! customAttr "aria-label" "52-week writing activity heatmap"
-     ++ "</figcaption>"
+                 $ do
-     ++ "</figure>"
+                     mapM_ monthLabel allDays
+                     mapM_ dayCell    allDays
+            H.figcaption H.! A.class_ "heatmap-legend" $ do
+                "Less\xA0"
+                legendSvg
+                "\xA0More"
 
 -- ---------------------------------------------------------------------------
 -- Stats page sections
 -- ---------------------------------------------------------------------------
 
-renderMonthlyVolume :: Map.Map Day Int -> String
+renderMonthlyVolume :: Map.Map Day Int -> H.Html
 renderMonthlyVolume wordsByDay =
     section "volume" "Monthly volume" $
     let byMonth = Map.fromListWith (+)
@@ -230,71 +369,80 @@ renderMonthlyVolume wordsByDay =
             , let (y, m, _) = toGregorian day
             ]
     in  if Map.null byMonth
-        then "<p><em>No dated content yet.</em></p>"
+        then H.p (H.em "No dated content yet.")
         else
             let maxWC = max 1 $ maximum $ Map.elems byMonth
                 bar (y, m) =
                     let wc  = fromMaybe 0 (Map.lookup (y, m) byMonth)
                         pct = if wc == 0 then 0 else max 2 (wc * 100 `div` maxWC)
                         lbl = shortMonth m ++ " \x2019" ++ drop 2 (show y)
-                    in  "<div class=\"build-bar-row\">"
+                    in  H.div H.! A.class_ "build-bar-row" $ do
-                     ++ "<span class=\"build-bar-label\">" ++ lbl ++ "</span>"
+                            H.span H.! A.class_ "build-bar-label" $ txt lbl
-                     ++ "<span class=\"build-bar-wrap\"><span class=\"build-bar\" style=\"width:"
+                            H.span H.! A.class_ "build-bar-wrap" $
-                     ++ show pct ++ "%\"></span></span>"
+                                H.span H.! A.class_ "build-bar"
-                     ++ "<span class=\"build-bar-count\">"
+                                       H.! A.style (H.stringValue ("width:" ++ show pct ++ "%"))
-                     ++ (if wc > 0 then commaInt wc else "") ++ "</span>"
+                                     $ mempty
-                     ++ "</div>"
+                            H.span H.! A.class_ "build-bar-count" $
-            in  "<div class=\"build-bars\">" ++ concatMap bar (Map.keys byMonth) ++ "</div>"
+                                if wc > 0 then txt (commaInt wc) else mempty
+            in  H.div H.! A.class_ "build-bars" $
+                    mapM_ bar (Map.keys byMonth)
 
-renderCorpus :: [TypeRow] -> [PageInfo] -> String
+renderCorpus :: [TypeRow] -> [PageInfo] -> H.Html
 renderCorpus typeRows allPIs =
-    section "corpus" "Corpus" $ concat
+    section "corpus" "Corpus" $ do
-    [ dl [ ("Total words",       commaInt totalWords)
+        dl [ ("Total words",        txt (commaInt totalWords))
-         , ("Total pages",       commaInt (length allPIs))
+           , ("Total pages",        txt (commaInt (length allPIs)))
-         , ("Total reading time", rtStr totalWords)
+           , ("Total reading time", txt (rtStr totalWords))
-         , ("Average length",    commaInt avgWC ++ " words")
+           , ("Average length",     txt (commaInt avgWC ++ " words"))
-         , ("Median length",     commaInt medWC ++ " words")
+           , ("Median length",      txt (commaInt medWC ++ " words"))
-         ]
+           ]
-    , table ["Type", "Pages", "Words", "Reading time"]
+        table ["Type", "Pages", "Words", "Reading time"]
-        (map row typeRows)
+              (map row typeRows)
-        (Just ["Total", commaInt (sum (map trCount typeRows))
+              (Just [ "Total"
-              , commaInt totalWords, rtStr totalWords])
+                    , txt (commaInt (sum (map trCount typeRows)))
-    ]
+                    , txt (commaInt totalWords)
+                    , txt (rtStr totalWords)
+                    ])
   where
     hasSomeWC  = filter (\p -> piWC p > 0) allPIs
     totalWords = sum (map trWords typeRows)
-    avgWC = if null hasSomeWC then 0 else totalWords `div` length hasSomeWC
+    avgWC      = if null hasSomeWC then 0 else totalWords `div` length hasSomeWC
-    medWC = median (map piWC hasSomeWC)
+    medWC      = median (map piWC hasSomeWC)
-    row r = [trLabel r, commaInt (trCount r), commaInt (trWords r), rtStr (trWords r)]
+    row r = [ txt (trLabel r)
+            , txt (commaInt (trCount r))
+            , txt (commaInt (trWords r))
+            , txt (rtStr    (trWords r))
+            ]
 
-renderNotable :: [PageInfo] -> String
+renderNotable :: [PageInfo] -> H.Html
 renderNotable allPIs =
-    section "notable" "Notable" $ concat
+    section "notable" "Notable" $ do
-    [ "<p><strong>Longest</strong></p>"
+        H.p (H.strong "Longest")
-    , pageList (take 5 (sortBy (comparing (Down . piWC)) hasSomeWC))
+        pageList (take 5 (sortBy (comparing (Down . piWC)) hasSomeWC))
-    , "<p><strong>Shortest</strong></p>"
+        H.p (H.strong "Shortest")
-    , pageList (take 5 (sortBy (comparing piWC) hasSomeWC))
+        pageList (take 5 (sortBy (comparing piWC) hasSomeWC))
-    ]
   where
     hasSomeWC = filter (\p -> piWC p > 50) allPIs
-    pageList ps = "<ol class=\"build-page-list\">"
+    pageList ps = H.ol H.! A.class_ "build-page-list" $
-        ++ concatMap (\p -> "<li>" ++ link (piUrl p) (piTitle p)
+        mapM_ (\p -> H.li $ do
-                         ++ " \x2014 " ++ commaInt (piWC p) ++ " words</li>") ps
+                  pageLink (piUrl p) (piTitle p)
-        ++ "</ol>"
+                  txt (" \x2014 " ++ commaInt (piWC p) ++ " words")
+              ) ps
 
-renderStatsTags :: [(String, Int)] -> Int -> String
+-- | Renamed/aliased to 'renderTagsSection' below — kept as a name for
-renderStatsTags topTags uniqueCount =
+-- legacy call sites until they are migrated. Defining it as the same
-    section "tags" "Tags" $ concat
+-- function (instead of an independent copy) prevents the two from
-    [ dl [("Unique tags", commaInt uniqueCount)]
+-- drifting silently.
-    , table ["Tag", "Items"] (map row topTags) Nothing
+renderStatsTags :: [(String, Int)] -> Int -> H.Html
-    ]
+renderStatsTags = renderTagsSection
-  where row (t, n) = [link ("/" ++ t ++ "/") t, show n]
 
-statsTOC :: String
+statsTOC :: H.Html
-statsTOC = "<ol>\n" ++ concatMap item entries ++ "</ol>\n"
+statsTOC = H.ol $ mapM_ item entries
   where
-    item (i, t) = "<li><a href=\"#" ++ i ++ "\" data-target=\"" ++ i ++ "\">"
+    item (i, t) =
-               ++ t ++ "</a></li>\n"
+        H.li $ H.a H.! A.href (H.stringValue ("#" ++ i))
+                   H.! customAttr "data-target" i
+                 $ txt t
     entries = [ ("activity", "Writing activity")
               , ("volume",   "Monthly volume")
               , ("corpus",   "Corpus")
@@ -306,17 +454,28 @@ statsTOC = "<ol>\n" ++ concatMap item entries ++ "</ol>\n"
 -- IO: output directory walk
 -- ---------------------------------------------------------------------------
 
+-- | Recursively walk a directory, returning @(file, size)@ tuples for every
+-- regular file beneath it.
+--
+-- Symlinks (both files and directories) are skipped, so a stray
+-- @_site\/a -> _site@ doesn't trigger an infinite loop.
 walkDir :: FilePath -> IO [(FilePath, Integer)]
 walkDir dir = do
     entries <- listDirectory dir `catch` (\(_ :: IOException) -> return [])
     fmap concat $ forM entries $ \e -> do
         let path = dir </> e
-        isDir <- doesDirectoryExist path
+        isLink <- pathIsSymbolicLink path
-        if isDir
+                    `catch` (\(_ :: IOException) -> return False)
-            then walkDir path
+        if isLink
+            then return []
             else do
-                sz <- getFileSize path `catch` (\(_ :: IOException) -> return 0)
+                isDir <- doesDirectoryExist path
-                return [(path, sz)]
+                if isDir
+                    then walkDir path
+                    else do
+                        sz <- getFileSize path
+                                `catch` (\(_ :: IOException) -> return 0)
+                        return [(path, sz)]
 
 displayExt :: FilePath -> String
 displayExt path = case takeExtension path of
@@ -354,9 +513,13 @@ countLinesDir :: FilePath -> String -> (FilePath -> Bool) -> IO (Int, Int)
 countLinesDir dir ext skipPred = do
     entries <- listDirectory dir `catch` (\(_ :: IOException) -> return [])
     let files = filter (\e -> takeExtension e == ext && not (skipPred e)) entries
+    -- Use strict text IO so the file handle is released as soon as the
+    -- contents are read; the prior 'readFile' chained lazy IO under
+    -- 'forM', leaving every handle open until the loop forced 'lines'.
     ls <- fmap sum $ forM files $ \e -> do
-        content <- readFile (dir </> e) `catch` (\(_ :: IOException) -> return "")
+        content <- TIO.readFile (dir </> e)
-        return (length (lines content))
+                     `catch` (\(_ :: IOException) -> return T.empty)
+        return (length (T.lines content))
     return (length files, ls)
 
 getLocStats :: IO (Int, Int, Int, Int, Int, Int)
@@ -385,125 +548,116 @@ getGitStats = do
     return (commits, firstDate)
 
 -- ---------------------------------------------------------------------------
--- HTML rendering: section helpers
+-- HTML rendering: build page sections
 -- ---------------------------------------------------------------------------
 
-section :: String -> String -> String -> String
+renderContent :: [TypeRow] -> H.Html
-section id_ title body = concat
-    [ "<h2 id=\"", id_, "\">", title, "</h2>\n"
-    , body
-    ]
-
-table :: [String] -> [[String]] -> Maybe [String] -> String
-table headers rows mFoot = concat
-    [ "<table class=\"build-table\">"
-    , "<thead><tr>", concatMap (\h -> "<th>" ++ h ++ "</th>") headers, "</tr></thead>"
-    , "<tbody>", concatMap renderRow rows, "</tbody>"
-    , maybe "" renderFoot mFoot
-    , "</table>"
-    ]
-  where
-    renderRow cells = "<tr>" ++ concatMap (\c -> "<td>" ++ c ++ "</td>") cells ++ "</tr>"
-    renderFoot cells = "<tfoot><tr class=\"build-total\">"
-                    ++ concatMap (\c -> "<td>" ++ c ++ "</td>") cells
-                    ++ "</tr></tfoot>"
-
-dl :: [(String, String)] -> String
-dl pairs = "<dl class=\"build-meta\">"
-    ++ concatMap (\(k, v) -> "<dt>" ++ k ++ "</dt><dd>" ++ v ++ "</dd>") pairs
-    ++ "</dl>"
-
-link :: String -> String -> String
-link url title = "<a href=\"" ++ url ++ "\">" ++ title ++ "</a>"
-
--- ---------------------------------------------------------------------------
--- HTML rendering: sections
--- ---------------------------------------------------------------------------
-
-renderContent :: [TypeRow] -> String
 renderContent rows =
     section "content" "Content" $
-    table
+    table ["Type", "Count", "Words", "Reading time"]
-        ["Type", "Count", "Words", "Reading time"]
+          (map row rows)
-        (map row rows)
+          (Just [ "Total"
-        (Just ["Total", commaInt totalCount, commaInt totalWords, rtStr totalWords])
+                , txt (commaInt totalCount)
+                , txt (commaInt totalWords)
+                , txt (rtStr    totalWords)
+                ])
   where
     totalCount = sum (map trCount rows)
     totalWords = sum (map trWords rows)
-    row r = [ trLabel r
+    row r = [ txt (trLabel r)
-            , commaInt (trCount r)
+            , txt (commaInt (trCount r))
-            , commaInt (trWords r)
+            , txt (commaInt (trWords r))
-            , rtStr    (trWords r)
+            , txt (rtStr    (trWords r))
             ]
 
-renderPages :: [PageInfo] -> Maybe (String,String,String) -> Maybe (String,String,String) -> String
+renderPages :: [PageInfo]
+            -> Maybe (String, String, String)
+            -> Maybe (String, String, String)
+            -> H.Html
 renderPages allPIs mOldest mNewest =
-    section "pages" "Pages" $ concat
+    section "pages" "Pages" $ do
-    [ dl $
+        dl $
-        [ ("Total pages",    commaInt (length allPIs))
+            [ ("Total pages",    txt (commaInt (length allPIs)))
-        , ("Average length", commaInt avgWC ++ " words")
+            , ("Average length", txt (commaInt avgWC ++ " words"))
-        ] ++
+            ] ++
-        maybe [] (\(d,t,u) -> [("Oldest content", d ++ " \x2014 " ++ link u t)]) mOldest ++
+            maybe [] (\(d,t,u) -> [("Oldest content", datedLink d t u)]) mOldest ++
-        maybe [] (\(d,t,u) -> [("Newest content", d ++ " \x2014 " ++ link u t)]) mNewest
+            maybe [] (\(d,t,u) -> [("Newest content", datedLink d t u)]) mNewest
-    , "<p><strong>Longest</strong></p>"
+        H.p (H.strong "Longest")
-    , pageList (take 3 (sortBy (comparing (Down . piWC)) hasSomeWC))
+        pageList (take 3 (sortBy (comparing (Down . piWC)) hasSomeWC))
-    , "<p><strong>Shortest</strong></p>"
+        H.p (H.strong "Shortest")
-    , pageList (take 3 (sortBy (comparing piWC)         hasSomeWC))
+        pageList (take 3 (sortBy (comparing piWC)         hasSomeWC))
-    ]
   where
     hasSomeWC = filter (\p -> piWC p > 0) allPIs
     avgWC     = if null hasSomeWC then 0
                 else sum (map piWC hasSomeWC) `div` length hasSomeWC
-    pageList ps = "<ol class=\"build-page-list\">"
+    datedLink d t u = do
-        ++ concatMap (\p -> "<li>" ++ link (piUrl p) (piTitle p)
+        txt (d ++ " \x2014 ")
-                         ++ " \x2014 " ++ commaInt (piWC p) ++ " words</li>") ps
+        pageLink u t
-        ++ "</ol>"
+    pageList ps = H.ol H.! A.class_ "build-page-list" $
+        mapM_ (\p -> H.li $ do
+                  pageLink (piUrl p) (piTitle p)
+                  txt (" \x2014 " ++ commaInt (piWC p) ++ " words")
+              ) ps
 
-renderDistribution :: [Int] -> String
+renderDistribution :: [Int] -> H.Html
 renderDistribution wcs =
     section "distribution" "Word-length distribution" $
-    "<div class=\"build-bars\">" ++ concatMap bar buckets ++ "</div>"
+    H.div H.! A.class_ "build-bars" $ mapM_ bar buckets
   where
     bucketOf w
-        | w <  500 = 0 | w < 1000 = 1 | w < 2000 = 2 | w < 5000 = 3 | otherwise = 4
+        | w <  500 = 0
-    labels = ["&lt; 500", "500 \x2013 1k", "1k \x2013 2k", "2k \x2013 5k", "\x2265 5k"]
+        | w < 1000 = 1
+        | w < 2000 = 2
+        | w < 5000 = 3
+        | otherwise = 4
+    labels :: [H.Html]
+    labels = [ "< 500"
+             , "500 \x2013 1k"
+             , "1k \x2013 2k"
+             , "2k \x2013 5k"
+             , "\x2265 5k"
+             ]
     counts = foldr (\w acc -> Map.insertWith (+) (bucketOf w) (1 :: Int) acc)
-                   (Map.fromList [(i, 0 :: Int) | i <- [0..4]]) wcs
+                   (Map.fromList [(i, 0 :: Int) | i <- [0 .. 4]]) wcs
-    buckets  = [(labels !! i, fromMaybe 0 (Map.lookup i counts)) | i <- [0..4]]
+    buckets  = [(labels !! i, fromMaybe 0 (Map.lookup i counts)) | i <- [0 .. 4]]
     maxCount = max 1 (maximum (map snd buckets))
     bar (lbl, n) =
         let pct = n * 100 `div` maxCount
-        in concat
+        in  H.div H.! A.class_ "build-bar-row" $ do
-            [ "<div class=\"build-bar-row\">"
+                H.span H.! A.class_ "build-bar-label" $ lbl
-            , "<span class=\"build-bar-label\">", lbl, "</span>"
+                H.span H.! A.class_ "build-bar-wrap" $
-            , "<span class=\"build-bar-wrap\"><span class=\"build-bar\" style=\"width:"
+                    H.span H.! A.class_ "build-bar"
-            , show pct, "%\"></span></span>"
+                           H.! A.style (H.stringValue ("width:" ++ show pct ++ "%"))
-            , "<span class=\"build-bar-count\">", show n, "</span>"
+                         $ mempty
-            , "</div>"
+                H.span H.! A.class_ "build-bar-count" $ txt (show n)
-            ]
 
-renderTagsSection :: [(String, Int)] -> Int -> String
+renderTagsSection :: [(String, Int)] -> Int -> H.Html
 renderTagsSection topTags uniqueCount =
-    section "tags" "Tags" $ concat
+    section "tags" "Tags" $ do
-    [ dl [("Unique tags", commaInt uniqueCount)]
+        dl [("Unique tags", txt (commaInt uniqueCount))]
-    , table ["Tag", "Items"] (map row topTags) Nothing
+        table ["Tag", "Items"] (map row topTags) Nothing
-    ]
   where
-    row (t, n) = [link ("/" ++ t ++ "/") t, show n]
+    row (t, n) = [link ("/" ++ t ++ "/") t, txt (show n)]
 
-renderLinks :: Maybe (String, Int, String) -> Int -> Int -> String
+renderLinks :: Maybe (String, Int, String) -> Int -> Int -> H.Html
 renderLinks mMostLinked orphanCount total =
     section "links" "Links" $
-    dl $
+    dl
-        (case mMostLinked of
+        [ case mMostLinked of
-            Nothing        -> [("Most-linked page", "\x2014")]
+            Nothing        -> ("Most-linked page", "\x2014")
-            Just (u, n, t) -> [("Most-linked page",
+            Just (u, n, t) ->
-                                link u t ++ " (" ++ show n ++ " inbound links)")]) ++
+                ( "Most-linked page"
-        [ ("Orphan pages", commaInt orphanCount
+                , do pageLink u t
-                        ++ " of " ++ commaInt total
+                     txt (" (" ++ show n ++ " inbound links)")
-                        ++ " (" ++ pctStr orphanCount total ++ ")") ]
+                )
+        , ( "Orphan pages"
+          , txt (commaInt orphanCount
+                  ++ " of " ++ commaInt total
+                  ++ " (" ++ pctStr orphanCount total ++ ")")
+          )
+        ]
 
-renderEpistemic :: Int -> Int -> Int -> Int -> Int -> String
+renderEpistemic :: Int -> Int -> Int -> Int -> Int -> H.Html
 renderEpistemic total ws wc wi we =
     section "epistemic" "Epistemic coverage" $
     table
@@ -515,47 +669,54 @@ renderEpistemic total ws wc wi we =
         ]
         Nothing
   where
-    row label n = [label, show n ++ " / " ++ show total, pctStr n total]
+    row label n = [ txt label
+                  , txt (show n ++ " / " ++ show total)
+                  , txt (pctStr n total)
+                  ]
 
-renderOutput :: Map.Map String (Int, Integer) -> Int -> Integer -> String
+renderOutput :: Map.Map String (Int, Integer) -> Int -> Integer -> H.Html
 renderOutput grouped totalFiles totalSize =
     section "output" "Output" $
     table
         ["Type", "Files", "Size"]
         (map row (sortBy (comparing (Down . snd . snd)) (Map.toList grouped)))
-        (Just ["Total", commaInt totalFiles, formatBytes totalSize])
+        (Just [ "Total"
+              , txt (commaInt totalFiles)
+              , txt (formatBytes totalSize)
+              ])
   where
-    row (ext, (n, sz)) = [ext, commaInt n, formatBytes sz]
+    row (ext, (n, sz)) = [txt ext, txt (commaInt n), txt (formatBytes sz)]
 
-renderRepository :: Int -> Int -> Int -> Int -> Int -> Int -> Int -> String -> String
+renderRepository :: Int -> Int -> Int -> Int -> Int -> Int -> Int -> String -> H.Html
 renderRepository hf hl cf cl jf jl commits firstDate =
     section "repository" "Repository" $
     dl
-        [ ("Haskell",         commaInt hl ++ " lines across " ++ show hf ++ " files")
+        [ ("Haskell",            txt (commaInt hl ++ " lines across " ++ show hf ++ " files"))
-        , ("CSS",             commaInt cl ++ " lines across " ++ show cf ++ " files")
+        , ("CSS",                txt (commaInt cl ++ " lines across " ++ show cf ++ " files"))
-        , ("JavaScript",      commaInt jl ++ " lines across " ++ show jf ++ " files (excl. minified)")
+        , ("JavaScript",         txt (commaInt jl ++ " lines across " ++ show jf ++ " files (excl. minified)"))
-        , ("Total git commits", commaInt commits)
+        , ("Total git commits",  txt (commaInt commits))
-        , ("Repository started", firstDate)
+        , ("Repository started", txt firstDate)
         ]
 
-renderBuild :: String -> String -> String
+renderBuild :: String -> String -> H.Html
 renderBuild ts dur =
     section "build" "Build" $
     dl
-        [ ("Generated",          ts)
+        [ ("Generated",           txt ts)
-        , ("Last build duration", dur)
+        , ("Last build duration", txt dur)
         ]
 
 -- ---------------------------------------------------------------------------
 -- Static TOC (matches the nine h2 sections above)
 -- ---------------------------------------------------------------------------
 
-pageTOC :: String
+pageTOC :: H.Html
-pageTOC = "<ol>\n" ++ concatMap item sections ++ "</ol>\n"
+pageTOC = H.ol $ mapM_ item sections
   where
     item (id_, title) =
-        "<li><a href=\"#" ++ id_ ++ "\" data-target=\"" ++ id_ ++ "\">"
+        H.li $ H.a H.! A.href (H.stringValue ("#" ++ id_))
-        ++ title ++ "</a></li>\n"
+                   H.! customAttr "data-target" id_
+                 $ txt title
     sections =
         [ ("content",      "Content")
         , ("pages",        "Pages")
@@ -584,7 +745,7 @@ statsRules tags = do
             -- ----------------------------------------------------------------
             -- Load all content items
             -- ----------------------------------------------------------------
-            essays  <- loadAll ("content/essays/*.md"      .&&. hasNoVersion)
+            essays  <- loadAll (P.essayPattern             .&&. hasNoVersion)
             posts   <- loadAll ("content/blog/*.md"        .&&. hasNoVersion)
             poems   <- loadAll ("content/poetry/*.md"      .&&. hasNoVersion)
             fiction <- loadAll ("content/fiction/*.md"     .&&. hasNoVersion)
@@ -664,9 +825,9 @@ statsRules tags = do
             -- ----------------------------------------------------------------
             essayMetas <- mapM (getMetadata . itemIdentifier) essays
             postMetas  <- mapM (getMetadata . itemIdentifier) posts
-            let epMetas   = essayMetas ++ postMetas
+            let epMetas    = essayMetas ++ postMetas
-                epTotal   = length epMetas
+                epTotal    = length epMetas
-                ep f      = length (filter (isJust . f) epMetas)
+                ep f       = length (filter (isJust . f) epMetas)
                 withStatus = ep (lookupString "status")
                 withConf   = ep (lookupString "confidence")
                 withImp    = ep (lookupString "importance")
@@ -698,32 +859,33 @@ statsRules tags = do
             -- ----------------------------------------------------------------
             -- Assemble page
             -- ----------------------------------------------------------------
-            let content = concat
+            let htmlContent :: H.Html
-                    [ renderContent rows
+                htmlContent = do
-                    , renderPages allPIs oldestDate newestDate
+                    renderContent rows
-                    , renderDistribution allWCs
+                    renderPages allPIs oldestDate newestDate
-                    , renderTagsSection topTags uniqueTags
+                    renderDistribution allWCs
-                    , renderLinks mostLinkedInfo orphanCount (length allPIs)
+                    renderTagsSection topTags uniqueTags
-                    , renderEpistemic epTotal withStatus withConf withImp withEv
+                    renderLinks mostLinkedInfo orphanCount (length allPIs)
-                    , renderOutput outputGrouped totalFiles totalSize
+                    renderEpistemic epTotal withStatus withConf withImp withEv
-                    , renderRepository hf hl cf cl jf jl commits firstDate
+                    renderOutput outputGrouped totalFiles totalSize
-                    , renderBuild buildTimestamp lastBuildDur
+                    renderRepository hf hl cf cl jf jl commits firstDate
-                    ]
+                    renderBuild buildTimestamp lastBuildDur
-                plainText  = stripHtmlTags content
+                contentString = renderHtml htmlContent
-                wc         = length (words plainText)
+                plainText     = stripHtmlTags contentString
-                rt         = readingTime plainText
+                wc            = length (words plainText)
-                ctx        = constField "toc"          pageTOC
+                rt            = readingTime plainText
-                          <> constField "word-count"   (show wc)
+                ctx           = constField "toc"          (renderHtml pageTOC)
-                          <> constField "reading-time" (show rt)
+                             <> constField "word-count"   (show wc)
-                          <> constField "title"        "Build Telemetry"
+                             <> constField "reading-time" (show rt)
-                          <> constField "abstract"     "Per-build corpus statistics, tag distribution, \
+                             <> constField "title"        "Build Telemetry"
-                                                        \link analysis, epistemic coverage, output metrics, \
+                             <> constField "abstract"     "Per-build corpus statistics, tag distribution, \
-                                                        \repository overview, and build timing."
+                                                          \link analysis, epistemic coverage, output metrics, \
-                          <> constField "build"        "true"
+                                                          \repository overview, and build timing."
-                          <> authorLinksField
+                             <> constField "build"        "true"
-                          <> siteCtx
+                             <> authorLinksField
+                             <> siteCtx
 
-            makeItem content
+            makeItem contentString
                 >>= loadAndApplyTemplate "templates/essay.html"   ctx
                 >>= loadAndApplyTemplate "templates/default.html" ctx
                 >>= relativizeUrls
@@ -734,7 +896,7 @@ statsRules tags = do
   create ["stats/index.html"] $ do
         route idRoute
         compile $ do
-            essays  <- loadAll ("content/essays/*.md"      .&&. hasNoVersion)
+            essays  <- loadAll (P.essayPattern             .&&. hasNoVersion)
             posts   <- loadAll ("content/blog/*.md"        .&&. hasNoVersion)
             poems   <- loadAll ("content/poetry/*.md"      .&&. hasNoVersion)
             fiction <- loadAll ("content/fiction/*.md"     .&&. hasNoVersion)
@@ -773,27 +935,28 @@ statsRules tags = do
 
             today <- unsafeCompiler (utctDay <$> getCurrentTime)
 
-            let content = concat
+            let htmlContent :: H.Html
-                    [ section "activity" "Writing activity" (renderHeatmap wordsByDay today)
+                htmlContent = do
-                    , renderMonthlyVolume wordsByDay
+                    section "activity" "Writing activity" (renderHeatmap wordsByDay today)
-                    , renderCorpus typeRows allPIs
+                    renderMonthlyVolume wordsByDay
-                    , renderNotable allPIs
+                    renderCorpus typeRows allPIs
-                    , renderStatsTags topTags uniqueTags
+                    renderNotable allPIs
-                    ]
+                    renderStatsTags topTags uniqueTags
-                plainText = stripHtmlTags content
+                contentString = renderHtml htmlContent
-                wc        = length (words plainText)
+                plainText     = stripHtmlTags contentString
-                rt        = readingTime plainText
+                wc            = length (words plainText)
-                ctx       = constField "toc"          statsTOC
+                rt            = readingTime plainText
-                         <> constField "word-count"   (show wc)
+                ctx           = constField "toc"          (renderHtml statsTOC)
-                         <> constField "reading-time" (show rt)
+                             <> constField "word-count"   (show wc)
-                         <> constField "title"        "Writing Statistics"
+                             <> constField "reading-time" (show rt)
-                         <> constField "abstract"     "Writing activity, corpus breakdown, \
+                             <> constField "title"        "Writing Statistics"
-                                                      \and tag distribution — computed at build time."
+                             <> constField "abstract"     "Writing activity, corpus breakdown, \
-                         <> constField "build"        "true"
+                                                          \and tag distribution — computed at build time."
-                         <> authorLinksField
+                             <> constField "build"        "true"
-                         <> siteCtx
+                             <> authorLinksField
+                             <> siteCtx
 
-            makeItem content
+            makeItem contentString
                 >>= loadAndApplyTemplate "templates/essay.html"   ctx
                 >>= loadAndApplyTemplate "templates/default.html" ctx
                 >>= relativizeUrls

build/Tags.hs

@@ -15,12 +15,13 @@
 module Tags
     ( buildAllTags
     , applyTagRules
-    , tagLinksField
     ) where
 
 import Data.List   (intercalate, nub)
 import Hakyll
-import Pagination  (pageSize, sortAndGroup)
+import Pagination  (sortAndGroup)
+import Patterns    (tagIndexable)
+import Contexts    (abstractField, tagLinksField)
 
 
 -- ---------------------------------------------------------------------------
@@ -64,9 +65,7 @@ tagIdentifier = fromFilePath . tagFilePath
 -- | Scan all essays and blog posts and build the Tags index.
 buildAllTags :: Rules Tags
 buildAllTags =
-    buildTagsWith getExpandedTags allContent tagIdentifier
+    buildTagsWith getExpandedTags tagIndexable tagIdentifier
-  where
-    allContent = ("content/essays/*.md" .||. "content/essays/*/index.md" .||. "content/blog/*.md") .&&. hasNoVersion
 
 
 -- ---------------------------------------------------------------------------
@@ -77,6 +76,7 @@ tagItemCtx :: Context String
 tagItemCtx =
     dateField "date" "%-d %B %Y"
     <> tagLinksField "item-tags"
+    <> abstractField
     <> defaultContext
 
 -- | Page identifier for a tag index page.
@@ -106,18 +106,3 @@ applyTagRules tags baseCtx = tagsRules tags $ \tag pat -> do
                 >>= relativizeUrls
 
 
--- ---------------------------------------------------------------------------
--- Tag links context field
--- ---------------------------------------------------------------------------
-
--- | List context field exposing an item's own (non-expanded) tags as
---   @tag-name@ / @tag-url@ objects.
---
---   $for(essay-tags)$<a href="$tag-url$">$tag-name$</a>$endfor$
-tagLinksField :: String -> Context a
-tagLinksField fieldName = listFieldWith fieldName itemCtx $ \item ->
-    map toItem <$> getTags (itemIdentifier item)
-  where
-    toItem t = Item (tagIdentifier t) t
-    itemCtx  = field "tag-name" (return . itemBody)
-            <> field "tag-url"  (\i -> return $ "/" ++ itemBody i ++ "/")

build/Utils.hs

@@ -1,10 +1,26 @@
 {-# LANGUAGE GHC2021 #-}
+{-# LANGUAGE OverloadedStrings #-}
+-- | Shared utilities used across the build system.
+--
+-- The HTML escapers (one for 'String', one for 'Text') live here so that
+-- every filter, context, and renderer goes through the same definition.
+-- The expansion order matters: @&@ MUST be replaced first, otherwise the
+-- @&@ injected by other rules gets re-escaped to @&@. The
+-- pure-character-by-character implementation used here avoids that hazard
+-- entirely (each character is mapped exactly once).
 module Utils
     ( wordCount
     , readingTime
     , escapeHtml
+    , escapeHtmlText
+    , trim
+    , authorSlugify
+    , authorNameOf
     ) where
 
+import           Data.Char (isAlphaNum, isSpace, toLower)
+import qualified Data.Text as T
+
 -- | Count the number of words in a string (split on whitespace).
 wordCount :: String -> Int
 wordCount = length . words
@@ -14,13 +30,49 @@ wordCount = length . words
 readingTime :: String -> Int
 readingTime s = max 1 (wordCount s `div` 200)
 
--- | Escape HTML special characters: <, >, &, ", '.
+-- | Escape HTML special characters: @&@, @<@, @>@, @\"@, @\'@.
+--
+-- Safe for use in attribute values and text content. The order of the
+-- @case@ branches is irrelevant — each input character maps to exactly
+-- one output sequence.
 escapeHtml :: String -> String
 escapeHtml = concatMap escChar
   where
+    escChar '&'  = "&amp;"
     escChar '<'  = "&lt;"
     escChar '>'  = "&gt;"
-    escChar '&'  = "&amp;"
     escChar '"'  = "&quot;"
     escChar '\'' = "&#39;"
     escChar c    = [c]
+
+-- | 'Text' counterpart of 'escapeHtml'.
+escapeHtmlText :: T.Text -> T.Text
+escapeHtmlText = T.concatMap escChar
+  where
+    escChar '&'  = "&amp;"
+    escChar '<'  = "&lt;"
+    escChar '>'  = "&gt;"
+    escChar '"'  = "&quot;"
+    escChar '\'' = "&#39;"
+    escChar c    = T.singleton c
+
+-- | Strip leading and trailing whitespace.
+trim :: String -> String
+trim = dropWhile isSpace . reverse . dropWhile isSpace . reverse
+
+-- | Lowercase a string, drop everything that isn't alphanumeric or
+-- space, then replace runs of spaces with single hyphens.
+--
+-- Used for author URL slugs (e.g. @"Levi Neuwirth" → "levi-neuwirth"@).
+-- Centralised here so 'Authors' and 'Contexts' cannot drift on Unicode
+-- edge cases.
+authorSlugify :: String -> String
+authorSlugify = map (\c -> if c == ' ' then '-' else c)
+              . filter (\c -> isAlphaNum c || c == ' ')
+              . map toLower
+
+-- | Extract the author name from a "Name | url" frontmatter entry.
+-- The URL portion is dropped (it's no longer used by the author system,
+-- which routes everything through @/authors/{slug}/@).
+authorNameOf :: String -> String
+authorNameOf s = trim (takeWhile (/= '|') s)

cabal.project.freeze

@@ -2,7 +2,7 @@ active-repositories: hackage.haskell.org:merge
 constraints: any.Glob ==0.10.2,
              any.HUnit ==1.6.2.0,
              any.JuicyPixels ==3.3.9,
-             any.OneTuple ==0.4.2,
+             any.OneTuple ==0.4.2.1,
              any.Only ==0.1,
              any.QuickCheck ==2.15.0.1,
              any.StateVar ==1.2.2,
@@ -182,7 +182,7 @@ constraints: any.Glob ==0.10.2,
              any.text-conversions ==0.3.1.1,
              any.text-icu ==0.8.0.5,
              any.text-iso8601 ==0.1.1,
-             any.text-short ==0.1.6,
+             any.text-short ==0.1.6.1,
              any.th-abstraction ==0.6.0.0,
              any.th-compat ==0.1.7,
              any.th-expand-syns ==0.4.12.0,

content/colophon.md

@@ -60,7 +60,7 @@ A full accounting of what this build process has actually produced is available
 ## The Computing Environment
 
 ::: dropcap
-Every tool I use was chosen rather than accepted. This distinction matters: the default path through the software ecosystem, particularly for developers, routes through choices made by convenience, employer mandate, or inertia rather than deliberation. I have consistently refused that path — not out of contrarianism, but because I find that the tools one uses become constitutive of the work one produces. This site is downstream of those choices in every particular.
+I am, like many passionate nerds within the realm of computing, obsessive over my technological choices. They are the subject of constant critique, review, revision, etc. I believe in the value of putting deep thought into the systems that one interacts with, rather than accepting the first showing of convenience and going with the flow. A system interacted with is an experience moreso than a mere tool.
 :::
 
 ### Desktop
@@ -72,23 +72,21 @@ My primary desktop is a rig I built myself, running **Gentoo Linux** with **Hypr
 - It is, in my experience, the best-maintained Linux distribution I have ever used.
 - The community is phenomenal.
 
-I have strong hardware preferences to match: [AMD]{.smallcaps} processors and graphics throughout. This is not tribal loyalty — I have used multiple distinct products from each major vendor and formed the preference empirically.
+I have strong hardware preferences to match; [AMD]{.smallcaps} hardware is used in favor of Intel and NVIDIA. I have used at least 2 distinct chips from each manufacturer and consistently find that, as far as x86-64 is concerned, AMD is the clear winner. As for my preference for AMD gpus, not only do I quite disagree with the business direction of NVIDIA, but the VRAM offerings are simply superior from AMD.
 
 ### Laptop
 
-For mobile computing, I use a [P]{.smallcaps}-series ThinkPad running **Arch Linux** — the same Hyprland environment, the same *Levshell*, the same muscle memory, but without the compilation overhead. Gentoo is impractical on battery-constrained hardware: compilation times are simply too long, and running the compiler continuously on battery is not a reasonable tradeoff. Arch is a sound alternative. Portage is better than pacman, but pacman on a laptop is entirely correct.
+For mobile computing, I use a [P]{.smallcaps}-series ThinkPad running **Arch Linux** — the same Hyprland environment, the same *Levshell*, the same muscle memory down to the config file. Gentoo is impractical on battery-constrained hardware, as compilation times are simply too long and require active power connection. Arch is a sound alternative, configurable enough to pass. Portage is better than pacman in my opinion, but pacman is still far better than horrid package managers like apt.
-
-The Hyprland environment runs identically on both machines. This is deliberate — I do not want to maintain two workflows. Every keybinding, every visual detail, every tool behaves the same. The continuity is itself a productivity commitment.
 
 ### Editor
 
-Everything on this site — every word of prose, every line of Haskell, every [CSS]{.smallcaps} rule — was written in **Emacs**. I use Emacs for the same reason I use Gentoo: it is configurable to a degree that other editors treat as pathological. Running `make watch` alongside an Emacs buffer gives something close to a [WYSIWYG]{.smallcaps} experience for this workflow: save the file, the Hakyll watcher recompiles, the browser updates. The loop is tight enough that the editor and the rendered output feel nearly continuous.
+Everything on this site — every word of prose, every line of Haskell, every [CSS]{.smallcaps} rule — was written in **Emacs**. I have used most of the major editors, and consistently experiment with others, but have yet to find any which come close to the power of Emacs. I intend to complete a project called "Pmacs," which will introduce much moderner parallelization, among other features, to Emacs. This is a project I intend to tackle in the Summer of 2026 at high intensity.
 
 ### Privacy-First Computing
 
 My email and [VPN]{.smallcaps} are self-hosted; I use Thunderbird as a client for the former. For browsing I use [LibreWolf](https://librewolf.net/), not Firefox: the Chromium monopoly and Mozilla's evident incompetence at browser development are, to me, equally concerning developments, and LibreWolf is the most coherent response to both. My phone runs [GrapheneOS](https://grapheneos.org/) — the only reasonably secure and private option for a mobile device, and one whose restrictions are, frankly, a feature rather than a limitation.
 
-The principle underlying all of these choices is the same one underlying the site's **No Tracking** policy: privacy is an architectural decision, not a settings toggle. You build the infrastructure first. Bolting on privacy after the fact, whether in a browser or on a website, is not privacy — it is the appearance of privacy.
+The principle underlying all of these choices is the same one underlying the site's **No Tracking** policy: privacy is an architectural decision, not a settings toggle. Bolting on privacy after the fact, whether in a browser or on a website, is not privacy — it is the appearance of privacy.
 
 ---
 
@@ -161,5 +159,4 @@ The tradition of the personal website is one that is built on a sense of communi
 This site is unfinished. Several portals have no content yet. The annotated bibliography
 is sparse. I am in the progress of migrating content, so stay tuned!
 
-The colophon itself is a living document. When the site changes substantially, this
+The colophon itself is a living document. When the site changes substantially, this page will change with it. The git repository on Forgejo (hosted on the git subdomain here) should always be considered to take precedence.
-page will change with it. The git history functions as an authoritative record; this page is my personal annotated summary.

content/drafts/essays/modern_idolatry.md

@@ -0,0 +1,41 @@
+---
+title: "The Modern Idolatry"
+date: 2026-04-06
+abstract: >
+  Thoughts on idolizing notions of success, whether extrinsic or intrinsic, prompted by my upcoming graduation from Brown University and a recent week spent in Paris.  
+tags:
+  - miscellany
+  - philosophy
+  - personal
+  - personal/travel
+authors:
+  - "Levi Neuwirth | /me.html"
+status: "Draft"
+history:
+  - date: "2026-04-06"
+---
+
+Travel affects me profoundly, and the effect is strangely uniform. There is a hierarchical structure of dichotomies that seems to define most aspects of my life, and my interactions with place are no exception to this rule. One of the dichotomies is as follows: I am rather accustomed to moving around in my adult life to date, never spending more than 4 months in a place before spending at least a few weeks somewhere else, and yet I rapidly develop a sense of "home" wherever I am - a stagnation of sorts, an acceptance of the region in which I reside and an abstraction away of the remainder of the world to some vast, estoeric TERRA INCOGNITA. Perhaps the most profound, persistent personal effect of travel on me is that it knocks me out of this mental state of spatial hibernation, reminding me that there is an entire world beyond that which I consistently perceive, and that I have the means to do something to have a positive impact on it. This has been a profoundly important sensation for me to have for many years now, and is thus one basis by which travel is consistently a high priority for me. 
+
+This is often combined with a sense of grand melancholy, the sort that for me is nearly ubiquitous in the presence of grandeur and beauty. It is a different incarnation of the same melancholy^[I should emphasize here that while "melancholy" may in general invoke a negative connotation, I do not feel that this is a negative emotion whatsoever. To me, the primary effect of melancholy, or at least melancholy of this sort, is an amplification of the imposing impetus, usually some sense of grandeur. The melancholy is like delicate cinnamon powder added to the top of a pristine flat white.] that I feel when I listen to a profound piece of music, view a painting that I enjoy, or reach the summit of a mountain that I have been embracing for hours. In this case the strength is perhaps yielded by the confluence of grandeur of the natural world - the vastness of space, the mystery of distinct regions that I have yet to know and the warm embrace of returning to those which I know but not well - and that of the human world - the various cultures, languages, beliefs, institutions, and above all people that are present in various places. 
+
+This grand, amplified melancholy typically has three causes in my life, two of which I have already mentioned. The third is instances of outward-facing "success" - I typically feel melancholic and pensive when I have done something or crossed some milestone^["Milestones" are not terms that I would use nor guidelines or aspects of some personal timeline or plan, but rather things that society imposes. They don't mean much to me on a personal level, but do unavoidably impact how I feel, since I cannot avoid societial influences as much as I sometimes wish I could.] that many folks see as an indicator of success (or the potential for it). One might imagine, then, that I felt quite a sensation as I was travelling in Paris during my most recent spring break, on the verge of graduating from Brown University after four years of work and extreme personal growth, and such an imagination would be highly warranted. As I took endless walks on the [Champ de Mars](https://en.wikipedia.org/wiki/Champ_de_Mars) and along the [Seine](https://en.wikipedia.org/wiki/Seine) many thoughts and musings were prompted by the grand sensations of emotion, grandeur, and wonder that I felt. They are largely concentrated around the theme of modern idolatry in the name of "success" and the impliciations of this, on both a personal and broader philosophical and societal level. My attempts to collect them into a format that I can share follow. 
+
+## Dichotomies
+<figure class="prose-excerpt">
+<blockquote>
+
+"Everything is a dichotomy; that is perhaps the grandeur of life, of the Universe itself." 
+
+
+</blockquote>
+<figcaption>Levi's personal journal, 29 January 2026</figcaption>
+</figure>
+
+::: dropcap
+What of "success" do I understand, and what of it have I cumulatively failed to understand? Of course, this question depends on one's chosen definition of "success," so perhaps the most interesting approach is to parameterize our choice of definition. Indeed, SUCCESS is a concept that means different things to different people, so perhaps such parameterization is implicitly necessary. Yet such parameterization unsettles me greatly on a personal level. It is the first example of dichotomy that we, together, may explore. 
+:::
+
+Society widely seems to view success as the fulfillment of goals rooted in extrinsic motivations. The credentialist nature of our society seems to conflate one's ability to earn a title with competence, experience, and, in some cases, worthiness - and who, exactly, is worthy of success, or, rather, is it success that deems one worthy in the eyes of the world? In more ways than one, it seems that we have been conditioned somehow through our institutions, both explicit and implicit, to conflate worthiness with success, and this conflation is perhaps grounded in the idea that success will be transitative; that is, one's continued association with successful people leads to more successful outcomes. This seems to imply that "success" is somehow a communal thing, inherently extrinsic that it diffuses and saturates, so long as those who have it^[For the sake of illustration here we are assuming that "success" is something to be had, a notion that will be debunked later.] are willing to continue associating with those who have less of it. 
+
+Yet this is in direct contrast to what is arguably the foundation of our^[I use "our" here to refer to citizens of the United States, my country of birth and the culture that largely influenced my perception of success.] success. The extrinsic nature of such success is not problematic, but the communal aspect is. The ethos of the [American Dream](https://en.wikipedia.org/wiki/American_Dream) is largely that of individualism - the promise that dense individual effort leads to success.

content/essays/beyond-comorbidity-indices.md

@@ -1,216 +0,0 @@
----
-title: "Beyond Comorbidity Indices"
-date: 2026-03-28
-abstract: >
-  A permutation-invariant deep-learning model that learns ICD-10-CM code representations improved 30-day readmission prediction (AUC 0.7496 vs 0.6553 for CCI) and postdischarge in-hospital mortality prediction (AUC 0.8557 vs 0.7844 for age-adjusted CCI) compared with standard comorbidity-index baselines in a national claims database of over 51 million adult hospitalizations.
-tags:
-  - research
-  - research/machine-learning
-authors:
-  - "Levi Neuwirth | /me.html"
-  - "Liqi Shu"
-  - "Xilin Wang"
-  - "Henry Zheng"
-affiliation:
-  - "Department of Neurology, Warren Alpert Medical School, Brown University"
-  - "Department of Computer Science, Brown University | https://cs.brown.edu"
-  - "Department of Mathematics, Brown University | https://mathematics.brown.edu/"
-  - "Department of Computer Science, Northeastern University"
-status: "Durable"
-confidence: 80
-importance: 3
-evidence: 5
-scope: average
-novelty: moderate
-practicality: moderate
-history:
-  - date: "2026-03-28"
-    note: Preprint auto-formatted for levineuwirth.org
----
-
-::: {.annotation .annotation--collapsible}
-**KEY POINTS**
-
-**Question.** Among adult hospitalizations in a national claims database, does a permutation-invariant model that learns ICD-10-CM representations improve prediction of 30-day outcomes compared with Charlson and Elixhauser comorbidity indices?
-
-**Findings.** In a temporally held-out national cohort (2021--2022), the ICD-10-CM embedding model achieved higher discrimination than comorbidity-index models for 30-day unplanned readmission (AUC, 0.7496) and 30-day postdischarge in-hospital mortality (AUC, 0.8557). The highest-performing comorbidity-index comparators achieved AUCs of 0.6553 and 0.7844, respectively.
-
-**Meaning.** Learning representations directly from ICD-10-CM codes may improve claims-based risk adjustment and help prioritize transitional-care resources at discharge.
-:::
-
-## Introduction
-
-::: dropcap
-Accurate prediction and risk adjustment for short-term clinical outcomes, such as 30-day hospital mortality and readmission, are critical for enhancing healthcare research quality, allowing fair assessment of healthcare outcomes and quality metrics [@cms_hrrp]. Most claims-based risk adjustment continues to rely on comorbidity indices such as the Charlson Comorbidity Index (CCI) and Elixhauser Comorbidity Index (ECI), which map diagnosis codes to a limited set of conditions [@charlson1987; @elixhauser1998]. While these indices are interpretable and widely deployed, they inevitably discard granularity and may miss clinically meaningful comorbidity patterns and interactions among diagnoses.
-:::
-
-Recent machine-learning approaches increasingly use high-dimensional ICD code inputs and have demonstrated improved prediction for a range of outcomes [@deschepper2020; @lelay2022; @qiao2022]. However, many approaches simplify or truncate ICD codes, aggregate diagnosis lists in ways that depend on code order, or are trained and evaluated in settings where coding practices differ across sites---each of which can limit robustness and transportability. In addition, many claims-based studies focus on in-hospital mortality and do not evaluate postdischarge mortality as a discharge-time outcome [@qiao2022; @davis2022; @harerimana2021; @matsui2022; @nguyen2017].
-
-We developed and temporally validated a claims-based prediction model that uses trainable ICD-10-CM embeddings and permutation-invariant aggregation of diagnosis lists. Using the Nationwide Readmissions Database (2016--2022), we assessed discrimination, calibration, and recall-weighted performance for 30-day unplanned readmission and 30-day postdischarge in-hospital mortality and compared results with Charlson and Elixhauser comorbidity-index models; we also generated diagnosis-level attributions using Integrated Gradients.
-
-## Methods
-
-### Study Design, Data Source, and Oversight
-
-We conducted a retrospective cohort study using the Healthcare Cost and Utilization Project (HCUP) Nationwide Readmissions Database (NRD), 2016--2022. Adult discharges from 2016--2020 were used for model development, and discharges from 2021--2022 were reserved for temporal external testing. Discharges in December of each year were excluded to allow complete 30-day follow-up within the same calendar year.
-
-Use of the NRD was governed by the HCUP data use agreement. Because the NRD contains deidentified data, the institutional review board determined the study was not human participants research and that informed consent was not required.
-
-### Cohort Definition
-
-We included hospitalizations for patients aged 18 years or older with a valid patient linkage identifier within each calendar year. For mortality analyses, index hospitalizations with in-hospital death were excluded from the primary outcome definition (postdischarge in-hospital mortality) and examined in a prespecified secondary analysis.
-
-### Outcomes
-
-The coprimary outcomes were (1) 30-day unplanned readmission and (2) 30-day postdischarge in-hospital mortality within 30 days of discharge. Readmissions were classified as unplanned using the HCUP algorithm. Postdischarge mortality was defined as inpatient death occurring during a subsequent hospitalization within 30 days after discharge; deaths outside the hospital are not captured in the NRD.
-
-### Predictors
-
-For each index hospitalization, we used up to 40 ICD-10-CM diagnosis codes (principal and secondary diagnoses). Diagnosis codes were label-encoded into integer identifiers for model input. Demographic and socioeconomic covariates included age, sex, primary payer, and ZIP-code median income quartile. Age was standardized; categorical variables (sex, payer, income quartile) were one-hot encoded with explicit handling of missing values. No diagnosis codes were filtered, simplified, or reordered.
-
-### Model Development
-
-#### Embedding Model Architecture
-
-The embedding model mapped each ICD-10-CM code to a trainable embedding vector and used a Deep Sets architecture [@zaheer2017] for permutation-invariant aggregation. The Deep Sets encoder processed individual diagnosis embeddings independently through shared multilayer perceptrons (MLPs); outputs were summed (permutation-invariant pooling) and passed to a decoder MLP. Demographic and socioeconomic covariates were processed through a separate 2-layer MLP and concatenated with the Deep Sets output before the final predictor MLP. The model was implemented in TensorFlow [@abadi2016] and trained with binary cross-entropy loss, the Adam optimizer, and early stopping on validation loss.
-
-#### Training Strategy
-
-Models were trained separately for each outcome. To address outcome imbalance, we randomly downsampled majority-class encounters in the training set to a 1:1 case-control ratio (validation and temporal test sets were not downsampled). Predicted probabilities were recalibrated on the validation set using logistic calibration. Hyperparameters were tuned via random search (32 trials per outcome), prioritizing validation AUC with $F_2$ as a secondary criterion.[^hparams]
-
-[^hparams]: Hyperparameter search details and final selected configurations are provided in the supplementary eMethods 1 and eTable 1.
-
-### Comparator Models
-
-We implemented logistic regression models based on the Charlson and Elixhauser comorbidity indices. For the Charlson model, we used both the unweighted comorbidity count and the traditional age-adjusted score [@ahrq_elixhauser; @fernando2019; @quan2005; @deyo1992; @quan2011; @stagg2006]. For the Elixhauser model, we used the unweighted comorbidity count; the refined AHRQ algorithm was applied for ICD-10-CM mapping [@ahrq_elixhauser]. All comparator models included age, sex, primary payer, and income quartile as covariates.
-
-### Statistical Analysis and Performance Evaluation
-
-Primary performance evaluation used a prespecified stratified random subsample of 2021--2022 discharges (n = 3,226,831; sampling fraction 0.10). Discrimination was assessed with AUC-ROC and 95% CIs (DeLong method); pairwise comparisons used DeLong tests [@youden1950; @delong1988]. Calibration was evaluated with calibration plots and the Brier score. Binary classification thresholds were selected on the validation set by maximizing the Youden index and applied unchanged to the temporal test set. Threshold-dependent metrics included sensitivity, specificity, precision, $F_1$, and $F_2$ (which weights recall twice as heavily as precision).
-
-### Interpretability Analysis
-
-We used Integrated Gradients [@sundararajan2017] to generate code-level attributions, quantifying each ICD-10-CM code's contribution to predicted risk. Attributions were averaged across occurrences for the 10 most positively and negatively influential codes per outcome (minimum 50 occurrences in the interpretability cohort).[^ig]
-
-[^ig]: Additional details on training, testing, and interpretability methods are provided in supplementary eMethods 1--3.
-
-### Ablation Studies
-
-We conducted three prespecified ablation studies to evaluate the contribution of key architectural choices: (1) addition of transformer blocks for attention-based contextualization, (2) replacement of Deep Sets with a permutation-variant flattening comparator, and (3) removal of demographic and socioeconomic covariates.[^ablation]
-
-[^ablation]: Full ablation details and results are in supplementary eMethods 4 and eTable 3.
-
-## Results
-
-### Cohort Characteristics
-
-The study included 19,120,000 adult hospitalizations from 2016--2020 (development cohort) and 32,268,308 from 2021--2022 (temporal test cohort). The 30-day unplanned readmission rate was 11.0% in the development cohort and 10.7% in the temporal test cohort. The 30-day postdischarge mortality rate was 0.6% in both cohorts. Additional cohort characteristics are reported in Table 1.
-
-### Primary Performance Comparison
-
-For 30-day readmission, the embedding model achieved an AUC of 0.7496 (95% CI, 0.7488--0.7504), outperforming the Charlson model (AUC, 0.6553; 95% CI, 0.6544--0.6562; P < .001) and the Elixhauser model (AUC, 0.6363; 95% CI, 0.6353--0.6372; P < .001). For 30-day postdischarge in-hospital mortality, the embedding model achieved an AUC of 0.8557 (95% CI, 0.8532--0.8581) vs the best-performing comparator (age-adjusted Charlson: 0.7844; 95% CI, 0.7813--0.7874; P < .001). Performance metrics are summarized in Table 2.
-
-The embedding model also showed superior recall-weighted performance. For 30-day readmission, $F_2$ was 0.4848 vs 0.4066 for the best comparator; for postdischarge mortality, $F_2$ was 0.0530 vs 0.0480. Calibration plots demonstrated good agreement between predicted and observed risks across the probability range.[^calibration]
-
-[^calibration]: Calibration reliability plots are provided in supplementary eFigure 2.
-
-::: {.annotation .annotation--static}
-**Figure 1 --- [placeholder]** Receiver operating characteristic curves for 30-day readmission (left) and 30-day postdischarge in-hospital mortality (right), comparing the embedding model against Charlson and Elixhauser comparators on the temporal test set.
-:::
-
-::: {.annotation .annotation--static}
-**Figure 2 --- [placeholder]** Calibration reliability plots for the embedding model and comparators on the temporal test set.
-:::
-
-### Interpretability Analysis
-
-Integrated Gradients attributions identified clinically relevant patterns. For readmission, codes indicating prior readmissions, chronic conditions requiring ongoing management, and social determinants (e.g., housing issues) showed high positive attributions. For postdischarge mortality, codes reflecting severe illness (e.g., sepsis, respiratory failure) and palliative care had high positive attributions, while codes for routine procedures (e.g., colonoscopy) had negative attributions.
-
-::: {.annotation .annotation--static}
-**Figure 3 --- [placeholder]** Top 10 positively and negatively attributed ICD-10-CM codes by mean Integrated Gradients attribution for 30-day readmission.
-:::
-
-::: {.annotation .annotation--static}
-**Figure 4 --- [placeholder]** Top 10 positively and negatively attributed ICD-10-CM codes by mean Integrated Gradients attribution for 30-day postdischarge in-hospital mortality.
-:::
-
-### Ablation Studies
-
-Addition of transformer blocks did not improve discrimination or $F_2$ score for either outcome.[^transformer] Replacing Deep Sets with a permutation-variant flattening comparator reduced AUC (P < .001 for readmission; P = .014 for mortality) and $F_2$ score.[^flattening] Removing demographic and socioeconomic covariates slightly reduced performance (P = .020 for readmission; P < .001 for mortality).[^demographics]
-
-[^transformer]: Reported P values for AUROC differences were P < .001 for readmission and P = 0.57 for postdischarge mortality. Full results in supplementary eTable 3A.
-[^flattening]: Full results in supplementary eTable 3B.
-[^demographics]: Full results in supplementary eTable 3C.
-
-::: {.annotation .annotation--static}
-**Figure 5 --- [placeholder]** Ablation study results comparing the base embedding model against transformer-augmented, permutation-variant, and ICD-only variants for both outcomes.
-:::
-
-## Discussion
-
-In a large national claims database, a permutation-invariant embedding model that learned ICD-10-CM representations achieved higher discrimination than Charlson and Elixhauser comorbidity-index models for predicting 30-day unplanned readmission and 30-day postdischarge in-hospital mortality. The embedding model also showed better calibration and recall-weighted performance, supporting its potential utility for discharge-time risk stratification and claims-based risk adjustment.
-
-### Comparison With Prior Work
-
-Prior studies have demonstrated the value of machine learning for readmission and mortality prediction [@deschepper2020; @lelay2022; @qiao2022; @davis2022; @harerimana2021; @matsui2022; @nguyen2017]. However, many approaches rely on permutation-variant aggregation (e.g., recurrent networks or attention over ordered sequences), which can be sensitive to code ordering---a dimension that varies across sites and coders. Our permutation-invariant approach addresses this limitation and may improve transportability. In addition, many claims-based studies focus on in-hospital mortality and do not evaluate postdischarge mortality as a discharge-time outcome. Our focus on postdischarge mortality provides a more clinically relevant endpoint for discharge planning and transitional care.
-
-### Implications for Practice and Policy
-
-Readmission reduction is a key quality and policy goal, with financial penalties under the Hospital Readmissions Reduction Program [@cms_hrrp; @joynt2013; @desai2016; @zuckerman2017]. However, current risk adjustment often relies on comorbidity indices that may under-adjust for complexity, leading to unfair comparisons across hospitals serving different populations [@obermeyer2019; @kind2014; @joynt2011]. Our findings suggest that learning representations directly from ICD-10-CM codes could improve fairness and precision in risk adjustment.
-
-At the patient level, improved risk stratification at discharge could help prioritize transitional-care resources (e.g., care coordination, medication reconciliation, follow-up calls) to high-risk patients [@hansen2011; @coleman2006]. The interpretability analysis also highlights specific diagnoses that drive risk, which may inform discharge planning conversations.
-
-### Limitations
-
-Our study has several limitations. First, the NRD captures only readmissions to acute-care hospitals within the same state and does not include deaths outside the hospital; both outcomes are therefore underestimated. Second, the model was trained and evaluated in a single national database; external validation in other claims databases and prospective evaluation are needed to assess generalizability and clinical utility. Third, while Integrated Gradients provides code-level attributions, the embedding model remains less interpretable than simple comorbidity indices [@rudin2019]. Fourth, we did not incorporate additional predictors (e.g., laboratory values, vital signs, discharge disposition) that may be available in some settings and could further improve performance. Finally, residual confounding by unmeasured factors (e.g., social determinants, functional status) may affect model predictions and limit clinical deployment without further validation.
-
-### Conclusions
-
-In a large national claims database, a permutation-invariant model that learned ICD-10-CM representations improved prediction of 30-day readmission and postdischarge in-hospital mortality compared with Charlson and Elixhauser index models. These findings support the use of high-dimensional diagnosis information for claims-based risk adjustment and discharge-time risk stratification, with prospective evaluation needed before clinical deployment.
-
-## Tables
-
-### Table 1: Cohort Characteristics {#table-1}
-
-| Characteristic | Development (2016--2020) | Temporal Test (2021--2022) |
-|:---|---:|---:|
-| Total hospitalizations | 19,120,000 | 32,268,308 |
-| 30-day readmission rate (%) | 11.0 | 10.7 |
-| 30-day postdischarge mortality rate (%) | 0.6 | 0.6 |
-
-### Table 2: Model Performance Comparison (Temporal Test Set) {#table-2}
-
-| Outcome | Model | AUC-ROC | 95% CI | Precision | Recall | $F_1$ | $F_2$ |
-|:---|:---|---:|:---:|---:|---:|---:|---:|
-| 30-day readmission | Embedding | 0.7496 | 0.7488--0.7504 | 0.1881 | 0.8006 | 0.3046 | 0.4848 |
-| | CCI | 0.6553 | 0.6544--0.6562 | 0.1493 | 0.6819 | 0.2453 | 0.4066 |
-| | CCI (age-adj) | 0.6483 | 0.6474--0.6491 | 0.1469 | 0.6794 | 0.2416 | 0.4016 |
-| | ECI | 0.6363 | 0.6353--0.6372 | 0.1426 | 0.6750 | 0.2357 | 0.3925 |
-| 30-day postdischarge mortality | Embedding | 0.8557 | 0.8532--0.8581 | 0.0111 | 0.8756 | 0.0220 | 0.0530 |
-| | CCI | 0.7217 | 0.7180--0.7253 | 0.0075 | 0.8026 | 0.0149 | 0.0371 |
-| | CCI (age-adj) | 0.7844 | 0.7813--0.7874 | 0.0093 | 0.7846 | 0.0185 | 0.0480 |
-| | ECI | 0.6686 | 0.6645--0.6728 | 0.0068 | 0.7901 | 0.0135 | 0.0336 |
-
-::: {.annotation .annotation--static}
-**Full title:** Development of an ICD-10-CM Embedding Model for Predicting 30-Day Readmission and Postdischarge In-Hospital Mortality in the Nationwide Readmissions Database
-
-**Keywords:** ICD-10-CM; readmission; mortality; claims data; risk adjustment; deep learning; model interpretability
-:::
-
-::: {.annotation .annotation--collapsible}
-**Structured Abstract**
-
-**Importance.** Comorbidity indices are widely used for claims-based risk adjustment but compress diagnostic information and may under-adjust for clinical complexity.
-
-**Objective.** To develop and temporally validate a permutation-invariant model that learns ICD-10-CM representations to predict 30-day unplanned readmission and 30-day postdischarge mortality and to compare performance with Charlson and Elixhauser comorbidity-index models.
-
-**Design, Setting, and Participants.** Retrospective cohort study of adult hospitalizations in the Healthcare Cost and Utilization Project Nationwide Readmissions Database (NRD), 2016--2022. Models were developed using discharges from 2016--2020 and temporally tested using 2021--2022 discharges. Primary performance evaluation was conducted in a prespecified stratified random subsample of 2021--2022 discharges (n = 3,226,831).
-
-**Exposure.** Up to 40 discharge diagnosis codes (ICD-10-CM) were mapped to trainable embeddings and aggregated with a permutation-invariant Deep Sets architecture; age, sex, primary payer, and ZIP code income quartile were also included as covariates.
-
-**Main Outcomes and Measures.** Outcomes were 30-day unplanned readmission and 30-day postdischarge in-hospital mortality. Discrimination was assessed with the area under the receiver operating characteristic curve (AUC) and 95% CIs; calibration and threshold-dependent metrics (including $F_2$) were evaluated. Performance was compared with optimized logistic regression models based on Charlson and Elixhauser indices.
-
-**Results.** In temporal testing, the embedding model showed higher discrimination for 30-day readmission (AUC, 0.7496 [95% CI, 0.7488--0.7504]) than Charlson (0.6553 [95% CI, 0.6544--0.6562]) and Elixhauser (0.6363 [95% CI, 0.6353--0.6372]). For 30-day postdischarge in-hospital mortality, the embedding model achieved an AUC of 0.8557 (95% CI, 0.8532--0.8581) vs the best-performing comparator (age-adjusted Charlson: 0.7844 [95% CI, 0.7813--0.7874]); DeLong tests were significant for each comparison (P < .001). Recall-weighted performance similarly favored the embedding model ($F_2$: 0.4848 vs 0.4066 for readmission; 0.0530 vs 0.0480 for postdischarge mortality).
-
-**Conclusions and Relevance.** In a large national claims database, a permutation-invariant model that learned ICD-10-CM representations improved prediction of 30-day readmission and postdischarge in-hospital mortality compared with Charlson and Elixhauser index models. These findings support the use of high-dimensional diagnosis information for claims-based risk adjustment and discharge-time risk stratification, with prospective evaluation needed before clinical deployment.
-:::

content/essays/beyond-comorbidity-indices/index.md

@@ -0,0 +1,367 @@
+---
+title: "Beyond Comorbidity Indices"
+date: 2026-04-09
+abstract: >
+  A deep learning model using ICD-10-CM diagnosis codes with a permutation-invariant Deep Sets aggregator improved 30-day unplanned readmission (AUC 0.7496 vs 0.6553 for CCI) and 30-day postdischarge in-hospital mortality (AUC 0.8557 vs 0.7844 for age-adjusted CCI) compared with Charlson and Elixhauser comorbidity-index benchmarks in a national claims database of over 113 million adult hospitalizations.
+tags:
+  - research
+  - research/machine-learning
+authors:
+  - "Levi Neuwirth | /me.html"
+  - "Liqi Shu"
+  - "Xilin Wang"
+  - "Henry Zheng"
+affiliation:
+  - "Department of Neurology, Warren Alpert Medical School, Brown University"
+  - "Department of Computer Science, Brown University | https://cs.brown.edu"
+  - "Department of Mathematics, Brown University | https://mathematics.brown.edu/"
+  - "Department of Computer Science, Northeastern University"
+status: "Durable"
+confidence: 80
+importance: 3
+evidence: 5
+scope: average
+novelty: moderate
+practicality: moderate
+bibliography: data/bci-paper.bib
+repository: "https://git.levineuwirth.org/neuwirth/beyond_comorbidity_indices"
+history:
+  - date: "2026-03-28"
+    note: Preprint auto-formatted for levineuwirth.org
+---
+
+::: {.annotation .annotation--collapsible}
+**KEY POINTS**
+
+**Question.** Among adult hospitalizations in a national claims database, does a deep learning model using ICD-10-CM diagnosis codes improve prediction of 30-day unplanned readmission and 30-day postdischarge in-hospital mortality compared with benchmark models based on Charlson and Elixhauser comorbidity indices?
+
+**Findings.** In this cohort study of 3,226,831 temporally held-out discharges, the ICD-10-CM--based model showed better discrimination than benchmark comorbidity-index models for both outcomes.
+
+**Meaning.** Using the full set of discharge diagnosis codes may improve short-term claims-based outcome prediction beyond summary comorbidity indices.
+:::
+
+## Introduction (Background and Significance)
+
+::: dropcap
+Accurate prediction and risk adjustment for short-term clinical outcomes, such as 30-day mortality and readmission, are critical for enhancing healthcare research quality, allowing fair assessment of healthcare outcomes and quality metrics [@cms_hrrp]. Most claims-based risk adjustment continues to rely on comorbidity indices such as the Charlson Comorbidity Index (CCI) and Elixhauser Comorbidity Index (ECI), which map diagnosis codes to a limited set of conditions [@charlson1987; @elixhauser1998]. While these indices are interpretable and widely deployed, they inevitably discard granularity and may miss clinically meaningful comorbidity patterns and interactions among diagnoses.
+:::
+
+Recent machine-learning approaches increasingly use a set of ICD-10-CM diagnosis codes and have demonstrated improved prediction for a range of outcomes [@deschepper2020; @lelay2022; @qiao2022]. However, many approaches simplify or truncate ICD codes, aggregate diagnosis lists in ways that depend on code order, or are trained and evaluated in settings where coding practices differ across sites---each of which can limit generalizability across settings. In addition, many claims-based studies focus on in-hospital mortality and do not evaluate postdischarge mortality among outcomes relevant at the time of discharge [@qiao2022; @davis2022; @harerimana2021; @matsui2022; @nguyen2017].
+
+In this study, we developed and temporally validated a claims-based deep learning model using ICD-10-CM diagnosis codes to predict 30-day unplanned readmission and 30-day postdischarge mortality in the Nationwide Readmissions Database. We compared its performance with benchmark models based on the Charlson and Elixhauser comorbidity indices, which are widely used for claims-based risk adjustment but were not originally designed for these specific outcomes. We also evaluated the model with different architectural design and examined diagnosis-level contributions to model predictions.
+
+## Materials and Methods
+
+### Study Design, Data Source, and Oversight
+
+We conducted a retrospective cohort study using the Healthcare Cost and Utilization Project (HCUP) Nationwide Readmissions Database (NRD), 2016--2022. Adult discharges from 2016 through 2020 were used for model development, and a later temporally separated cohort from 2021 through 2022 was reserved for temporal validation. Discharges in December of each year were excluded to allow complete 30-day follow-up within the same calendar year.
+
+Use of the NRD was governed by the HCUP data use agreement. Because the NRD contains deidentified data, the institutional review board determined the study was not human participants research and that informed consent was not required.
+
+### Cohort Definition
+
+We included hospitalizations for patients aged 18 years or older with a valid patient linkage identifier within each calendar year. For both the readmission and mortality analyses, index hospitalizations ending in in-hospital death were excluded because patients were not at risk for postdischarge outcomes. In-hospital death during the index hospitalization was examined in a prespecified secondary mortality analysis (eResults 1).
+
+### Outcomes
+
+The coprimary outcomes were (1) 30-day unplanned readmission and (2) 30-day postdischarge in-hospital mortality (hereafter, postdischarge mortality). Readmissions were classified as unplanned if they were coded as nonelective admissions in the HCUP database. Postdischarge mortality was defined as inpatient death occurring during a subsequent hospitalization within 30 days after discharge. Deaths outside the hospital are not captured in the NRD.
+
+### Predictors
+
+For each index hospitalization, we used up to 40 ICD-10-CM diagnosis codes (principal and secondary) and patient-level covariates (age, sex, primary payer, and ZIP-code median income quartile). Age was standardized, and categorical variables were represented using one-hot encoding. Analyses were restricted to records with nonmissing outcome ascertainment and complete covariates.
+
+### Comparator Models
+
+For benchmarking, we computed the Elixhauser Comorbidity Index (ECI) and Charlson Comorbidity Index (CCI) for each index hospitalization and treated each index as a continuous risk score [@charlson1987; @elixhauser1998]. The ECI identifies 30+ distinct conditions from administrative data, serving as a critical tool for risk adjustment in studies evaluating in-hospital mortality and short-term readmissions [@elixhauser1998; @ahrq_elixhauser; @fernando2019; @quan2005]. The CCI consolidates up to 19 comorbid conditions into a weighted numeric score, including variants that adjust for age, primarily predicting long-term mortality and readmissions [@charlson1987; @fernando2019; @quan2005; @deyo1992; @quan2011]. The ECI was computed using an ICD-10-CM--adapted AHRQ approach that identifies chronic comorbidities primarily from secondary diagnoses [@quan2005]. The CCI was computed using ICD-10-CM mappings to 17 comorbidity categories; both raw CCI and age-adjusted CCI were evaluated [@stagg2006]. These benchmark models used the index score alone as the predictor; age, sex, primary payer, and ZIP-code income quartile were not added separately. Discrimination and threshold-dependent classification metrics were derived directly from the score distributions, with operating thresholds selected on the validation set and then applied unchanged to the temporal test evaluation subsample.
+
+### Model Architecture
+
+We developed a deep learning framework that embeds each patient's diagnosis list along with demographic and socioeconomic information to predict the outcome. Each ICD-10-CM code was mapped into a dense vector representation through a learned numerical transformation. To obtain a single representation for each patient while avoiding reliance on diagnosis ordering, we used an aggregation approach that does not depend on code order:
+
+$$f(x) = \rho\!\left(\sum_{x \in X} \phi(x)\right)$$
+
+where $X$ denotes the set of embedded diagnosis vectors. Functions $\phi$ and $\rho$ were implemented as multilayer perceptrons with ReLU activations [@zaheer2017].
+
+Demographic and socioeconomic variables were processed via a separate 2-layer multilayer perceptron. The resulting vector was concatenated with the aggregated diagnosis representation and passed through fully connected layers with ReLU activations and dropout regularization. A sigmoid output layer finally produced a predicted probability for each outcome.
+
+### Model Development and Temporal Validation
+
+Data from 2016--2020 were split into training (90%) and validation (10%) sets. For each outcome, models were trained to minimize binary cross-entropy loss. To address class imbalance, majority-class downsampling was applied during training (see Supplementary eMethods 1). Because majority-class downsampling altered the effective outcome prevalence in the training data, predicted probabilities were corrected using the original training-set prevalence before reporting calibration, temporal-test probabilities, and web-calculator outputs [@pozzolo2015]. This deterministic correction affects probability scaling but not rank-based discrimination. Hyperparameters (embedding dimension, Deep Sets depth/width, demographic tower width, predictor multilayer perceptron configuration, and dropout rate) were tuned using random search; the configuration with best validation AUROC (with recall-weighted metrics used as secondary criteria) was selected (see Supplementary eTable 1).
+
+Temporal validation was based on eligible 2021--2022 discharges. To support computational feasibility while preserve outcome prevalence, primary performance evaluation was conducted in a prespecified stratified random subsample of the eligible 2021--2022 temporal test cohort, with 10% of outcome-positive and 10% of outcome-negative discharges sampled for each outcome (Supplementary eMethods 2). Models were implemented in Python using TensorFlow [@abadi2016].
+
+### Performance Metrics
+
+For threshold-dependent metrics, binary classification thresholds were selected on the validation set by maximizing the Youden index (sensitivity + specificity − 1) and then applied unchanged to the temporal test evaluation subsample for each model [@youden1950].
+
+Because outcomes were imbalanced, we emphasized discrimination and precision--recall performance. Primary metrics included AUROC with 95% confidence intervals (CIs), average precision, precision, recall, $F_1$ score, and $F_2$ score (placing greater weight on recall).
+
+### Statistical Analysis
+
+AUROCs and their 95% CIs were estimated using DeLong's nonparametric method [@delong1988]. Pairwise comparisons in AUROC between the embedding model and each comorbidity-index comparator were performed using DeLong tests for correlated ROC curves [@delong1988]. Resulting $P$ values are unadjusted and interpreted alongside effect sizes and 95% CIs.
+
+We conducted prespecified ablation analyses to estimate the incremental contribution of key model components, including addition of transformer blocks, replacement of the order-invariant Deep Sets aggregator with a permutation-variant flattening comparator, and removal of demographic and socioeconomic inputs; details are provided in Supplementary eMethods 4.
+
+### Model Interpretation
+
+We used Integrated Gradients (IG) to estimate code-level contributions to model predictions for each outcome [@sundararajan2017; @placido2023]. Attribution values were summarized at the ICD-10-CM code level, with positive values indicating higher predicted risk and negative values indicating lower predicted risk. To reduce instability from rare codes, ranked summaries were restricted to codes with at least 50 occurrences in the temporal test evaluation subsample. Additional implementation details are provided in Supplementary eMethods 3.
+
+### Web Application
+
+A public, read-only web calculator accepts discharge diagnosis lists and returns risk estimates with code-level explanations; inputs are not stored. The tool is intended for research and demonstration purposes rather than clinical decision-making. The calculator is available at: <https://levineuwirth.github.io/icd_embeddings/>. Implementation details are provided in Supplementary eFigure 4.
+
+## Results
+
+### Cohort size and event prevalence
+
+The NRD included 80,217,696 discharges in 2016--2020 for model development and 33,322,761 discharges in 2021--2022 for temporal testing (Figure 1). After application of outcome-specific eligibility criteria, the validation cohort included 7,828,015 discharges. Primary performance evaluation was conducted in a prespecified stratified random subsample of 3,226,831 discharges from the eligible 2021--2022 temporal test cohort, and this evaluation subsample was not downsampled. For model training, majority-class downsampling was applied to address class imbalance, yielding analytic training samples of 17,200,994 discharges for the readmission analysis and 544,138 discharges for the postdischarge mortality analysis. In the temporal test evaluation subsample, 30-day unplanned readmission occurred in 362,696 discharges (11.2%), and 30-day postdischarge in-hospital mortality occurred in 13,071 discharges (0.4%).
+
+### Model Performance
+
+Detailed performance metrics for the ICD-10-CM--based model and benchmark comorbidity-index models are shown in Table 1. In the temporal test evaluation subsample, the ICD-10-CM--based model showed higher discrimination than comparator models for both 30-day unplanned readmission and 30-day postdischarge mortality (Figure 2). For readmission, the AUROC was 0.750 (95% CI, 0.749--0.750) for the ICD-10-CM--based model, compared with 0.655 (95% CI, 0.654--0.656) for the CCI model, 0.644 (95% CI, 0.644--0.645) for the age-adjusted CCI model, and 0.636 (95% CI, 0.635--0.637) for the ECI model. For postdischarge mortality, the AUROC was 0.856 (95% CI, 0.853--0.858) for the ICD-10-CM--based model, compared with 0.784 (95% CI, 0.781--0.787) for the best-performing comparator, the age-adjusted CCI model; the AUROC for the ECI model was 0.641 (95% CI, 0.636--0.647). DeLong tests comparing the ICD-10-CM--based model with each comorbidity-index comparator were significant for all pairwise comparisons ($P < .001$). Calibration curves showed overall agreement between predicted and observed risk for both outcomes, with greater deviation at higher predicted-risk ranges; this deviation was less pronounced for postdischarge mortality than for readmission (Figure 3).
+
+At the prespecified threshold selected on the validation set, the ICD-10-CM--based model showed higher recall-weighted performance than comparator models, with $F_2$ scores of 0.485 vs 0.407 for 30-day readmission and 0.053 vs 0.048 for postdischarge mortality. Threshold-dependent metrics, including precision, recall, and specificity, are shown in Table 1. Because the classification threshold was selected using the Youden index, these metrics reflect a balance of sensitivity and specificity rather than optimization for a specific clinical use case. For readmission, these gains were accompanied by only modest precision, consistent with the difficulty of predicting this heterogeneous outcome.
+
+In the prespecified secondary analysis expanding mortality to include in-hospital death during the index hospitalization, the ICD-10-CM--based model achieved an AUROC of 0.965 (95% CI, 0.965--0.966), exceeding that of the best-performing comparator model (age-adjusted CCI: AUROC, 0.750 [95% CI, 0.749--0.751]) (eTable 2).
+
+### Ablation Studies
+
+We evaluated a set of prespecified model variants that removed or augmented architectural components (eg, ICD-only inputs and insertion of transformer blocks) to estimate the incremental contribution of each element. We also compared the order-invariant aggregation approach with an order-dependent flattening-based aggregator to quantify any performance tradeoff attributable to enforcing invariance. In covariate ablation, removing demographic and socioeconomic inputs (age, sex, payer, and ZIP-income quartile) caused modest attenuation in performance (readmission AUROC, 0.750 vs 0.748; postdischarge mortality AUROC, 0.856 vs 0.848; similar $F_2$ scores), suggesting that diagnosis patterns captured most, but not all, of the predictive signal. Implementation details are provided in Supplementary eMethods 4; results are summarized in eTable 3.
+
+### Feature Importance
+
+ICD-10-CM codes with the 10 highest positive and negative contributions to both prediction outcomes are shown in Figure 4. For 30-day readmission, acute myeloblastic leukemia, in relapse (C9202), had the greatest positive contribution, whereas encounter for care and examination of mother immediately after delivery (Z390) had the greatest negative contribution. For 30-day postdischarge mortality, C9202 also had the greatest positive contribution, whereas assault by unspecified sharp object, initial encounter (X999XXA) had the greatest negative contribution. The most influential diagnosis codes for 30-day mortality prediction including inpatient death are shown in Supplementary eFigure 2.
+
+## Discussion
+
+In this national claims-based cohort study, a deep learning model using the full set of discharge diagnosis codes showed better discrimination than benchmark models based on Charlson and Elixhauser comorbidity indices for both 30-day unplanned readmission and 30-day postdischarge in-hospital mortality. The performance gain was larger for postdischarge mortality than for readmission. Performance remained favorable in a later, temporally separated NRD cohort, supporting robustness across subsequent years of the same database [@davis2020; @collins2024]. At the same time, these comparisons should be interpreted as benchmarking against widely used summary comorbidity approaches rather than as head-to-head comparisons with models purpose-built for these exact outcomes.
+
+### Comparison with prior work
+
+This pattern is consistent with the structure of the compared methods. Charlson and Elixhauser indices compress diagnosis information into a limited set of predefined conditions and were designed primarily for broad case-mix adjustment rather than high-resolution outcome prediction [@charlson1987; @elixhauser1998]. By contrast, the present model learns from the full diagnosis-code set and can represent co-occurrence patterns that are not captured by summary indices [@morgan2019; @beam2018]. Unlike many prior deep-learning approaches that depend on richer electronic health record inputs and site-specific preprocessing, this framework was designed for portability within claims-based settings by using routinely available diagnosis, demographic, and payer-related variables [@rajkomar2018]. This design also preserves the broader diagnostic context of each hospitalization rather than reducing diagnoses to fixed summary weights as ECI and CCI.
+
+### Interpretability
+
+Interpretability in this setting should not be viewed as an afterthought to an otherwise opaque model. Using Integrated Gradients, the model provided code-level attributions that were generally clinically plausible and helped explain why predicted risk increased or decreased for a given patient. For example, diagnoses associated with high treatment burden or advanced systemic illness, such as relapsed acute myeloid leukemia and alcoholic cirrhosis with ascites, tended to increase predicted risk, whereas postpartum encounters and some assault-related injuries tended to decrease it. These findings suggest that learning-based models can yield clinically meaningful information rather than functioning only as "black boxes," even when they are more flexible than traditional summary indices [@sundararajan2017; @placido2023; @rudin2019].
+
+One plausible explanation for the performance gap between the present model and the Charlson and Elixhauser indices is that the prognostic contribution of a diagnosis is not fixed across patients. Summary comorbidity indices assign prespecified, static weights to diagnosis groups, effectively assuming that a given condition contributes similarly regardless of the broader diagnostic context. By contrast, in the present model, the contribution of a diagnosis could vary according to the full set of co-occurring diagnoses, which is more consistent with how risk is often understood clinically. We did not directly test this mechanism, so it should be interpreted as a hypothesis supported by the attribution patterns rather than as a proven explanation for the observed performance differences. Nevertheless, this dynamic view of diagnosis contribution may help explain why retaining the full diagnosis-code context improved prediction beyond summary comorbidity scores. As with other attribution methods, these explanations improve transparency but do not establish causality.
+
+### Clinical and policy implications
+
+These findings have two potential implications. First, in discharge-facing workflows, a claims-compatible model could be evaluated in read-only settings to identify patients who may warrant closer follow-up, medication reconciliation, or transitional-care outreach [@hansen2011; @coleman2006]. Second, in research and quality measurement, more granular use of diagnosis data may improve outcome prediction when summary comorbidity indices underrepresent diagnostic complexity [@joynt2013; @desai2016; @zuckerman2017]. This tool is intended for clinical prioritization and equitable quality measurement, not for coverage denial or utilization gatekeeping [@obermeyer2019].
+
+Because demographic and socioeconomic factors are known to influence postdischarge outcomes, we assessed their incremental contribution beyond diagnosis patterns using ablation [@kind2014; @joynt2011]. Removing age, sex, payer, and neighborhood income produced minimal changes in performance, suggesting that much of the predictive signal available to this model was already captured by diagnosis patterns. This finding should not be interpreted to mean that demographic or socioeconomic factors are unimportant. Rather, within this claims-based framework, coded diagnoses may already capture part of the risk signal associated with demographic and socioeconomic differences, whether through differences in disease burden, comorbidity clustering, or patterns of healthcare use.
+
+The public read-only calculator is intended for research and demonstration rather than clinical deployment. Future work should focus on external validation, prospective evaluation in read-only workflows, monitoring for coding and case-mix drift, and recalibration when needed [@davis2020; @collins2024; @collins2015].
+
+### Limitations
+
+This study has several limitations. First, the NRD captures deaths only during inpatient encounters; therefore, the mortality outcome reflects postdischarge in-hospital mortality rather than all-cause 30-day mortality. Second, claims data are subject to coding error and variation and do not directly capture functional status, physiologic severity, or many social risk factors. Third, although temporal validation in later NRD years reduces optimism, it is not a substitute for external validation, and performance may differ in other health systems or data sources with different coding practices, case mix, and discharge workflows. Fourth, this study evaluated predictive performance rather than downstream improvement in confounding control, hospital profiling, or other risk-adjustment applications; thus, better discrimination does not by itself establish superior risk adjustment, and because the model was trained specifically for 30-day unplanned readmission and postdischarge in-hospital mortality, performance may not generalize to other outcomes without separate validation. Fifth, Charlson and Elixhauser indices were included as benchmark comparators because of their widespread use in claims-based analyses, but they were not originally developed for these specific outcomes; accordingly, these comparisons should be interpreted as benchmarking rather than definitive head-to-head testing. Finally, attribution methods may improve transparency but do not establish causality [@rudin2019].
+
+## Conclusions
+
+A deep learning model using ICD-10-CM diagnosis codes improved prediction of 30-day unplanned readmission and 30-day postdischarge mortality compared with Charlson and Elixhauser comorbidity-index models in the Nationwide Readmissions Database. Prospective validation, drift monitoring, and attention to intended use will be essential before implementation for clinical decision support or policy applications.
+
+## Data Sharing Statement
+
+The study used de-identified data from the Healthcare Cost and Utilization Project (HCUP) Nationwide Readmissions Database under a data-use agreement. Data are available from HCUP to qualified researchers.
+
+## Code Availability
+
+The analytic code (including the non-elective readmission implementation, model training, and evaluation) will be made publicly available at publication in a GitHub repository (<https://github.com/Rice-wxl/icd-10-embedding>), with a versioned release tag/commit to support reproducibility. HCUP NRD data cannot be shared by the authors under the data-use agreement.
+
+## Conflict of Interest Disclosures
+
+The authors report no conflicts of interest related to this work.
+
+## Tables
+
+### Table 1: Performance metrics for the ICD model vs. CCI and ECI {#table-1}
+
+Performance metrics for the ICD model vs. CCI and ECI for 30-day readmission (a) and 30-day postdischarge mortality (b) in the temporal test evaluation subsample.
+
+**(a) 30-day readmission**
+
+| Methods                        | AUC-ROC                      | Accuracy | Precision  | Recall     | $F_1$      | $F_2$      |
+|:-------------------------------|:-----------------------------|---------:|-----------:|-----------:|-----------:|-----------:|
+| ICD Model (Threshold: 0.5022)  | **0.7496** [0.7488, 0.7504]  |   0.5892 | **0.1881** | **0.8006** | **0.3046** | **0.4848** |
+| CCI                            | 0.6553 [0.6544, 0.6562]      | **0.6962** | 0.1844   | 0.4973     | 0.2690     | 0.3713     |
+| CCI Age-Adjusted               | 0.6444 [0.6435, 0.6453]      |   0.6479 | 0.1673     | 0.5360     | 0.2550     | 0.3720     |
+| ECI                            | 0.6363 [0.6353, 0.6372]      |   0.5708 | 0.1598     | 0.6622     | 0.2575     | 0.4066     |
+
+**(b) 30-day postdischarge mortality**
+
+| Methods                        | AUC-ROC                      | Accuracy   | Precision  | Recall     | $F_1$      | $F_2$      |
+|:-------------------------------|:-----------------------------|-----------:|-----------:|-----------:|-----------:|-----------:|
+| ICD Model (Threshold: 0.4644)  | **0.8557** [0.8532, 0.8581]  |     0.6848 | **0.0111** | **0.8756** | **0.0220** | **0.0530** |
+| CCI                            | 0.7621 [0.7585, 0.7657]      |     0.6987 | 0.0093     | 0.6963     | 0.0184     | 0.0442     |
+| CCI Age-Adjusted               | 0.7844 [0.7813, 0.7874]      |     0.7352 | 0.0102     | 0.6700     | 0.0201     | 0.0480     |
+| ECI                            | 0.6414 [0.6358, 0.6469]      | **0.7763** | 0.0089     | 0.4915     | 0.0175     | 0.0415     |
+
+*Primary performance evaluation used a prespecified stratified random subsample of eligible 2021--2022 discharges. Classification thresholds were selected on the validation set by maximizing the Youden index and then applied unchanged to the temporal test evaluation subsample.*
+
+## Figures
+
+::: {.annotation .annotation--static}
+**Figure 1 --- [placeholder]** Flow chart of discharge records in NRD for training, validation, and testing cohorts. Primary performance evaluation used a prespecified stratified random subsample of eligible 2021--2022 discharges. This temporal-test evaluation subsample was not downsampled. Classification thresholds were selected on the validation set by maximizing the Youden index and then applied unchanged to the temporal test subsample.
+:::
+
+**Figure 2.** Receiver operating characteristic (ROC) curves and area under the curve (AUC) for 30-day readmission and postdischarge mortality in the temporal test evaluation subsample. Each curve depicts the trade-off between sensitivity and specificity across different thresholds.
+
+![(a) 30-day readmission](figures/fig2a-roc-readmission.png)
+
+![(b) 30-day postdischarge mortality](figures/fig2b-roc-mortality.png)
+
+**Figure 3.** Calibration curves on temporal test evaluation subsample for 30-day readmission and postdischarge mortality.
+
+![(a) 30-day readmission](figures/fig3a-calibration-readmission.png)
+
+![(b) 30-day postdischarge mortality](figures/fig3b-calibration-mortality.png)
+
+**Figure 4.** Top influential ICD codes for model prediction. Mean Integrated Gradients attribution per occurrence (positive values indicate higher predicted risk; negative values indicate lower predicted risk).
+
+![(a) 30-day readmission](figures/fig4a-ig-readmission.png)
+
+![(b) 30-day postdischarge mortality](figures/fig4b-ig-mortality.png)
+
+## Supplement
+
+### eMethods
+
+1. **Training and Hyperparameter Tuning**
+2. **Temporal Test Set Construction and Threshold Selection**
+3. **Integrated Gradients for Code-Level Attribution**
+4. **Ablation Analyses**
+   1. Transformer Blocks
+   2. Deep Sets vs Permutation-Variant Flattening Comparator
+   3. Demographic and Socioeconomic Inputs
+
+### eTables
+
+1. **Hyperparameter Configurations Used in Models**
+2. **Performance Comparison for 30-Day Mortality Including Index-Hospital Death**
+3. **Ablation Study Results**
+   - (A) Addition of Transformer Blocks
+   - (B) Replacement of Deep Sets With Flattening Comparator
+   - (C) Removal of Demographic and Socioeconomic Inputs (ICD-Only)
+
+### eFigures
+
+1. **Permutation-invariant ICD Embedding Model**
+2. **Top ICD-10-CM Codes by Integrated Gradients for 30-Day Mortality Including Index-Hospital Death**
+3. **Calibration Reliability Plots for Temporal Test Set Predictions**
+   - 30-Day Readmission
+   - 30-Day Postdischarge Mortality
+4. **Web Calculator Interface Examples**
+
+### eMethods 1. Training and Hyperparameter Tuning
+
+Models were trained using batch size 128 for 10 epochs with the Adam optimizer at a learning rate of 2e-5. Early stopping was applied with patience of 2 epochs, retaining the checkpoint with the best validation performance. To address outcome imbalance, we randomly downsampled majority-class encounters in the training set to achieve a target case-control ratio of 1:1 (validation data and temporal test evaluation subsample were not downsampled). Because majority-class downsampling changes the effective outcome prevalence and can bias predicted probabilities, we performed adjustment with the original downsampling ratio of the training set and use the readjusted model outputs in all metrics/plots and for the web calculator. Random seeds for the train/validation split, downsampling, and model initialization were set to ensure reproducibility.
+
+Hyperparameters were tuned via random search (32 trials per outcome). eTable 1 reports the selected configurations. Hyperparameter definitions: $d_{\text{embed}}$ (ICD embedding dimension); $d_{\text{hidden}}$ (Deep Sets hidden dimension); $r_{\text{deepset}} \times d_{\text{hidden}}$ (Deep Sets output dimension); $n_{\text{encode}}$ and $n_{\text{decode}}$ (numbers of Deep Sets encoding/decoding layers); $d_{\text{demo}}$ (first-layer width of the demographic/socioeconomic MLP; second layer set to $d_{\text{demo}}/2$); $d_{\text{mlp}}$ (first-layer width of the predictor MLP, halving each layer to a minimum of 32 over 4 layers); $r_{\text{dropout}}$ (dropout rate). Model selection prioritized validation AUROC; recall-weighted metrics (including $F_2$) were used as secondary criteria.
+
+### eMethods 2. Temporal Test Set Construction and Threshold Selection
+
+Temporal testing used eligible 2021--2022 data. To enable computationally feasible evaluation while preserving outcome prevalence, we created the temporal test evaluation subsample by stratified random sampling of the combined eligible 2021--2022 cohort, sampling 10% of outcome-positive and 10% of outcome-negative discharges for each outcome. This yielded approximately 3.2 million discharges for primary performance evaluation. Interpretability analyses used the same temporal test evaluation subsample.
+
+Binary classification thresholds for each model were selected on the validation set by maximizing the Youden index (sensitivity + specificity − 1) and then applied unchanged to the temporal test evaluation subsample.
+
+### eMethods 3. Integrated Gradients for Code-Level Attribution
+
+Integrated Gradients (IG) was used to quantify code-level influence on model predictions. The baseline input was defined as a neutral input corresponding to an empty diagnosis list (ie, no diagnosis codes). The straight-line interpolation path from baseline to the observed input was discretized into 32 steps. At each step, gradients of the model logit were computed with respect to diagnosis embeddings; gradients were accumulated across steps and summed across embedding dimensions to yield a scalar attribution per code occurrence. Attribution values retained sign, with positive values indicating higher predicted risk and negative values indicating lower predicted risk. To reduce instability from rare codes, ICD-10-CM codes with fewer than 50 total occurrences in the temporal test evaluation subsample were excluded from ranked summaries. For each outcome, we reported the 10 codes with the largest mean positive attributions and the 10 codes with the largest mean negative attributions.
+
+### eMethods 4. Ablation Analyses
+
+#### eMethods 4.1 Transformer blocks
+
+To evaluate whether attention-based contextualization improves performance, we added three multi-head transformer blocks operating over individual ICD embeddings. Each block followed a standard transformer design with multi-head attention, residual connections, normalization, and feed-forward sublayers. We used 3 attention heads, dropout 0.3, embedding dimension $d_{\text{embed}}$, and feed-forward dimension $4 \times d_{\text{embed}}$.
+
+Comparative results are shown in eTable 3, Panel A. Across both outcomes, transformer blocks did not materially improve AUROC and $F_2$ score relative to the base model. Reported $P$ values for AUROC differences were $P < .001$ for readmission and $P = 0.57$ for postdischarge mortality.
+
+#### eMethods 4.2 Deep Sets vs permutation-variant flattening comparator
+
+To test whether permutation invariance via Deep Sets reduced predictive performance, we compared the base model with a permutation-variant alternative: a flattening layer that converts the 2-dimensional ICD embedding matrix into a 1-dimensional vector, followed by two MLP layers with $d_{\text{hidden}}$ and $r_{\text{deepset}} \times d_{\text{hidden}}$ units to mirror the Deep Sets hidden/output sizes.
+
+Results are shown in eTable 3, Panel B. The base Deep Sets models outperformed the flattening comparators on AUROC and $F_2$ score. Reported $P$ values for AUROC differences were $P < .001$ for readmission and $P = 0.014$ for postdischarge mortality.
+
+#### eMethods 4.3 Demographic and socioeconomic inputs
+
+To evaluate the incremental value of non-diagnosis covariates, we removed the 2-layer demographic/socioeconomic MLP and trained ICD-only variants.
+
+Results are shown in eTable 3, Panel C. ICD-only variants had slightly worse AUROC and $F_2$ score. Reported $P$ values for AUROC differences were $P = 0.020$ for readmission and $P < .001$ for postdischarge mortality.
+
+### eTable 1: Hyperparameter configurations used in models
+
+| Outcome                                           | $d_{\text{embed}}$ | $d_{\text{hidden}}$ | $r_{\text{deepset}}$ | $n_{\text{encode}}$ | $n_{\text{decode}}$ | $d_{\text{demo}}$ | $d_{\text{mlp}}$ | $r_{\text{dropout}}$ |
+|:--------------------------------------------------|---:|----:|----:|---:|---:|---:|----:|----:|
+| 30-day readmission                                | 32 | 416 | 0.5 | 1  | 3  | 64 | 480 | 0.1 |
+| 30-day postdischarge mortality                    | 64 | 320 | 0.6 | 2  | 1  | 64 | 384 | 0.1 |
+| 30-day mortality including index-hospital death   | 64 | 416 | 0.8 | 3  | 3  | 64 | 448 | 0.4 |
+
+*The model configurations are determined through hyperparameter tuning for each outcome variable, respectively. All models share the same batch size and learning rate.*
+
+### eTable 2. Performance comparison for 30-day mortality including index-hospital death
+
+| Methods          | AUC-ROC                  | Precision | Recall | $F_1$  | $F_2$  |
+|:-----------------|:-------------------------|----------:|-------:|-------:|-------:|
+| ICD Model        | 0.9651 [0.9647, 0.9656]  | 0.2107    | 0.9165 | 0.3427 | 0.5489 |
+| CCI              | 0.7217 [0.7203, 0.7231]  | 0.0663    | 0.6270 | 0.1200 | 0.2331 |
+| CCI Age-Adjusted | 0.7501 [0.7489, 0.7513]  | 0.0724    | 0.6043 | 0.1294 | 0.2448 |
+| ECI              | 0.6158 [0.6139, 0.6177]  | 0.0637    | 0.4427 | 0.1114 | 0.2022 |
+
+### eTable 3. Ablation study results
+
+**(A) Addition of transformer blocks**
+
+| Outcome Variable               | Model Variant        | AUC-ROC | AUC-ROC CI       | Precision | Recall | $F_1$  | $F_2$  |
+|:-------------------------------|:---------------------|--------:|:-----------------|----------:|-------:|-------:|-------:|
+| 30-day readmission             | Full Model           | 0.7496  | [0.7488, 0.7504] | 0.1881    | 0.8006 | 0.3046 | 0.4848 |
+|                                | 3 Transformer Blocks | 0.7472  | [0.7464, 0.7479] | 0.1974    | 0.7565 | 0.3131 | 0.4829 |
+| 30-day postdischarge mortality | Full Model           | 0.8557  | [0.8532, 0.8581] | 0.0111    | 0.8756 | 0.0220 | 0.0530 |
+|                                | 3 Transformer Blocks | 0.8547  | [0.8523, 0.8572] | 0.0114    | 0.8662 | 0.0225 | 0.0542 |
+
+**(B) Replacement of Deep Sets with flattening comparator**
+
+| Outcome Variable               | Model Variant   | AUC-ROC | AUC-ROC CI       | Precision | Recall | $F_1$  | $F_2$  |
+|:-------------------------------|:----------------|--------:|:-----------------|----------:|-------:|-------:|-------:|
+| 30-day readmission             | Full Model      | 0.7496  | [0.7488, 0.7504] | 0.1881    | 0.8006 | 0.3046 | 0.4848 |
+|                                | Without DeepSet | 0.7474  | [0.7466, 0.7482] | 0.1933    | 0.7724 | 0.3092 | 0.4829 |
+| 30-day postdischarge mortality | Full Model      | 0.8557  | [0.8532, 0.8581] | 0.0111    | 0.8756 | 0.0220 | 0.0530 |
+|                                | Without DeepSet | 0.8513  | [0.8488, 0.8538] | 0.0108    | 0.8777 | 0.0214 | 0.0515 |
+
+**(C) Removal of demographic and socioeconomic inputs (ICD-only)**
+
+| Outcome Variable               | Model Variant   | AUC-ROC | AUC-ROC CI       | Precision | Recall | $F_1$  | $F_2$  |
+|:-------------------------------|:----------------|--------:|:-----------------|----------:|-------:|-------:|-------:|
+| 30-day readmission             | Full Model      | 0.7496  | [0.7488, 0.7504] | 0.1881    | 0.8006 | 0.3046 | 0.4848 |
+|                                | ICD Inputs Only | 0.7483  | [0.7475, 0.7490] | 0.1907    | 0.7868 | 0.3070 | 0.4842 |
+| 30-day postdischarge mortality | Full Model      | 0.8557  | [0.8532, 0.8581] | 0.0111    | 0.8756 | 0.0220 | 0.0530 |
+|                                | ICD Inputs Only | 0.8483  | [0.8457, 0.8509] | 0.0110    | 0.8627 | 0.0218 | 0.0525 |
+
+### eFigure 1: Permutation-invariant ICD Embedding Model
+
+![Given a patient's ICD-10-CM diagnosis codes together with demographic and socioeconomic features, the model estimates risk of 30-day readmission and 30-day postdischarge mortality. Diagnosis codes are embedded and aggregated with a Deep Sets module, then combined with other inputs to generate the final prediction.](figures/efig1-model-architecture.png)
+
+### eFigure 2: Top ICD-10-CM codes by Integrated Gradients for 30-day mortality including index-hospital death
+
+![Top ICD-10-CM codes by Integrated Gradients for 30-day mortality including index-hospital death.](figures/efig2-ig-mortality-with-inhospital.png)
+
+### eFigure 3. Calibration reliability plots for temporal test evaluation subsample predictions
+
+*(A) 30-day unplanned readmission and (B) 30-day postdischarge mortality.*
+
+::: {.annotation .annotation--static}
+**eFigure 3 --- [placeholder]** Calibration reliability plots for temporal test evaluation subsample predictions.
+:::
+
+### eFigure 4. Web Calculator Interface Examples
+
+*(A) With demographics and (B) Without demographics.*
+
+**(A)**
+
+![Web calculator interface with demographics.](figures/efig4a-calculator-with-demographics.png)
+
+**(B)**
+
+![Web calculator interface without demographics.](figures/efig4b-calculator-without-demographics.png)

data/bci-paper.bib

@@ -0,0 +1,359 @@
+% bci-paper.bib — Beyond Comorbidity Indices
+% BibLaTeX format. References for the "Deep Learning of Diagnosis Codes
+% for Readmission and Postdischarge Mortality Prediction" manuscript.
+% Numbered order matches the docx reference list.
+
+@misc{cms_hrrp,
+  author = {{Centers for Medicare \& Medicaid Services}},
+  title  = {Hospital Readmissions Reduction Program ({HRRP})},
+  url    = {https://www.cms.gov/medicare/payment/prospective-payment-systems/acute-inpatient-pps/hospital-readmissions-reduction-program-hrrp}
+}
+
+@article{charlson1987,
+  author  = {Charlson, M. E. and Pompei, P. and Ales, K. L. and MacKenzie, C. R.},
+  title   = {A new method of classifying prognostic comorbidity in longitudinal studies: development and validation},
+  journal = {Journal of Chronic Diseases},
+  year    = {1987},
+  volume  = {40},
+  number  = {5},
+  pages   = {373--383}
+}
+
+@article{elixhauser1998,
+  author  = {Elixhauser, A. and Steiner, C. and Harris, D. R. and Coffey, R. M.},
+  title   = {Comorbidity measures for use with administrative data},
+  journal = {Medical Care},
+  year    = {1998},
+  volume  = {36},
+  number  = {1},
+  pages   = {8--27}
+}
+
+@article{deschepper2020,
+  author  = {Deschepper, Mathieu and Eeckloo, Kristof and Vogelaers, Dominique and Waegeman, Willem},
+  title   = {Using structured pathology data to predict hospital-wide mortality at admission},
+  journal = {PLoS One},
+  year    = {2020},
+  volume  = {15},
+  number  = {6},
+  pages   = {e0235117}
+}
+
+@article{lelay2022,
+  author  = {Le Lay, Jonathan and Martin, Sylvain and Mosnier, Arnaud and others},
+  title   = {Prediction of hospital readmission of multimorbid patients using machine learning models},
+  journal = {PLoS One},
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+  number  = {12},
+  pages   = {e0279433}
+}
+
+@article{qiao2022,
+  author  = {Qiao, Edmund M. and Deng, Jie and Kluger, Harvey M. and Yu, James B. and Gross, Cary P.},
+  title   = {Evaluating High-Dimensional Machine Learning Models to Predict Hospital Mortality Among Older Patients With Cancer},
+  journal = {JCO Clinical Cancer Informatics},
+  year    = {2022},
+  volume  = {6},
+  pages   = {e2100186}
+}
+
+@article{davis2022,
+  author  = {Davis, Steve and Borah, Michael F. and Hansen, Justin and Malin, Bradley and Robinson, Jonathan and Turchin, Alexander},
+  title   = {Effective hospital readmission prediction models using machine-learned features},
+  journal = {BMC Health Services Research},
+  year    = {2022},
+  volume  = {22},
+  number  = {1},
+  pages   = {1415}
+}
+
+@article{harerimana2021,
+  author  = {Harerimana, Gaspard and Kim, Jong Wook and Jang, Beakcheol},
+  title   = {A deep attention model to forecast the Length Of Stay and the in-hospital mortality right on admission from {ICD} codes and demographic data},
+  journal = {Journal of Biomedical Informatics},
+  year    = {2021},
+  volume  = {118},
+  pages   = {103778}
+}
+
+@article{matsui2022,
+  author  = {Matsui, Hiroki and Yasunaga, Hideo and Fushimi, Kiyohide and Homma, Yuichi},
+  title   = {Development of Deep Learning Models for Predicting In-Hospital Mortality Using an Administrative Claims Database: Retrospective Cohort Study},
+  journal = {JMIR Medical Informatics},
+  year    = {2022},
+  volume  = {10},
+  number  = {2},
+  pages   = {e27936}
+}
+
+@article{nguyen2017,
+  author  = {Nguyen, Phuoc and Tran, Truyen and Wickramasinghe, Nilmini and Venkatesh, Svetha},
+  title   = {{Deepr}: A Convolutional Net for Medical Records},
+  journal = {IEEE Journal of Biomedical and Health Informatics},
+  year    = {2017},
+  volume  = {21},
+  number  = {1},
+  pages   = {22--30}
+}
+
+@misc{ahrq_elixhauser,
+  author = {{Agency for Healthcare Research and Quality}},
+  title  = {Elixhauser Comorbidity Software Refined for {ICD-10-CM}},
+  url    = {https://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp}
+}
+
+@article{fernando2019,
+  author  = {Fernando, Dulith T. and Berecki-Gisolf, Janneke and Newstead, Stuart and Ansari, Zul},
+  title   = {Effect of comorbidity on injury outcomes: a review of existing indices},
+  journal = {Annals of Epidemiology},
+  year    = {2019},
+  volume  = {36},
+  pages   = {5--14}
+}
+
+@article{quan2005,
+  author  = {Quan, Hude and Sundararajan, Vijaya and Halfon, Patricia and others},
+  title   = {Coding algorithms for defining comorbidities in {ICD-9-CM} and {ICD-10} administrative data},
+  journal = {Medical Care},
+  year    = {2005},
+  volume  = {43},
+  number  = {11},
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+}
+
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+  author  = {Deyo, Richard A. and Cherkin, Daniel C. and Ciol, Marcia A.},
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+}
+
+@article{quan2011,
+  author  = {Quan, Hude and Li, Bing and Couris, Chantal M. and others},
+  title   = {Updating and validating the {Charlson} comorbidity index and score for risk adjustment in hospital discharge abstracts using data from 6 countries},
+  journal = {American Journal of Epidemiology},
+  year    = {2011},
+  volume  = {173},
+  number  = {6},
+  pages   = {676--682}
+}
+
+@misc{stagg2006,
+  author    = {Stagg, Vince},
+  title     = {{CHARLSON}: {Stata} module to calculate {Charlson} index of comorbidity},
+  year      = {2006},
+  publisher = {Boston College Department of Economics}
+}
+
+@inproceedings{zaheer2017,
+  author    = {Zaheer, Manzil and Kottur, Satwik and Ravanbakhsh, Siamak and Poczos, Barnabas and Salakhutdinov, Ruslan and Smola, Alexander},
+  title     = {Deep Sets},
+  booktitle = {Advances in Neural Information Processing Systems},
+  year      = {2017},
+  volume    = {30}
+}
+
+@inproceedings{pozzolo2015,
+  author    = {Dal Pozzolo, Andrea and Caelen, Olivier and Johnson, Reid A. and Bontempi, Gianluca},
+  title     = {Calibrating Probability with Undersampling for Unbalanced Classification},
+  booktitle = {2015 {IEEE} Symposium Series on Computational Intelligence},
+  year      = {2015},
+  pages     = {159--166}
+}
+
+@inproceedings{abadi2016,
+  author    = {Abadi, Mart{\'i}n and Barham, Paul and Chen, Jianmin and Chen, Zhifeng and Davis, Andy and Dean, Jeffrey and Devin, Matthieu and Ghemawat, Sanjay and Irving, Geoffrey and Isard, Michael and Kudlur, Manjunath and Levenberg, Josh and Monga, Rajat and Moore, Sherry and Murray, Derek G. and Steiner, Benoit and Tucker, Paul and Vasudevan, Vijay and Warden, Pete and Wicke, Martin and Yu, Yuan and Zheng, Xiaoqiang},
+  title     = {{TensorFlow}: A System for Large-Scale Machine Learning},
+  booktitle = {Proceedings of the 12th {USENIX} Symposium on Operating Systems Design and Implementation},
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+  pages     = {265--283}
+}
+
+@article{youden1950,
+  author  = {Youden, W. J.},
+  title   = {Index for rating diagnostic tests},
+  journal = {Cancer},
+  year    = {1950},
+  volume  = {3},
+  number  = {1},
+  pages   = {32--35}
+}
+
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+  author  = {DeLong, Elizabeth R. and DeLong, David M. and Clarke-Pearson, Daniel L.},
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+  volume  = {44},
+  number  = {3},
+  pages   = {837--845}
+}
+
+@inproceedings{sundararajan2017,
+  author    = {Sundararajan, Mukund and Taly, Ankur and Yan, Qiqi},
+  title     = {Axiomatic Attribution for Deep Networks},
+  booktitle = {Proceedings of the 34th International Conference on Machine Learning},
+  year      = {2017},
+  pages     = {3319--3328}
+}
+
+@article{placido2023,
+  author  = {Placido, Davide and Yuan, Bo and Hjaltelin, Jessica X. and Zheng, Chunlei and Haue, Amalie D. and Chmura, Piotr J. and Yuan, Chen and Kim, Jihye and Umeton, Renato and Antell, Gregory and Chowdhury, Alexander and Franz, Alexandra and Brais, Lauren and Andrews, Elizabeth and Marks, Debora S. and Regev, Aviv and Ayandeh, Siamack and Brophy, Mary T. and Do, Nhan V. and Kraft, Peter and Wolpin, Brian M. and Rosenthal, Michael H. and Fillmore, Nathanael R. and Brunak, S{\o}ren and Sander, Chris},
+  title   = {A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories},
+  journal = {Nature Medicine},
+  year    = {2023},
+  volume  = {29},
+  number  = {5},
+  pages   = {1113--1122}
+}
+
+@article{davis2020,
+  author  = {Davis, Sharon E. and Greevy, Robert A. and Fonnesbeck, Christopher and Lasko, Thomas A. and Walsh, Colin G. and Matheny, Michael E.},
+  title   = {Detection of calibration drift in clinical prediction models to inform model updating},
+  journal = {Journal of Biomedical Informatics},
+  year    = {2020},
+  volume  = {112},
+  pages   = {103611}
+}
+
+@article{collins2024,
+  author  = {Collins, Gary S. and Dhiman, Paula and Ma, Jie and Schlussel, Michael M. and Archer, Lucinda and Van Calster, Ben and Harrell, Frank E. and Martin, Glen P. and Moons, Karel G. M. and van Smeden, Maarten and Sperrin, Matthew and Bullock, Garrett S. and Riley, Richard D.},
+  title   = {Evaluation of clinical prediction models (part 1): from development to external validation},
+  journal = {BMJ},
+  year    = {2024},
+  volume  = {384},
+  pages   = {e074819}
+}
+
+@article{morgan2019,
+  author  = {Morgan, Daniel J. and Bame, Bill and Zimand, Paul and Dooley, Patricia and Thom, Kerri A. and Harris, Anthony D. and Bentzen, S{\o}ren and Ettinger, Walter and Garrett-Ray, Stacy D. and Tracy, J. Kathleen and Liang, Yuanyuan},
+  title   = {Assessment of Machine Learning vs Standard Prediction Rules for Predicting Hospital Readmissions},
+  journal = {JAMA Network Open},
+  year    = {2019},
+  volume  = {2},
+  number  = {3},
+  pages   = {e190348}
+}
+
+@article{beam2018,
+  author  = {Beam, Andrew L. and Kohane, Isaac S.},
+  title   = {Big Data and Machine Learning in Health Care},
+  journal = {JAMA},
+  year    = {2018},
+  volume  = {319},
+  number  = {13},
+  pages   = {1317--1318}
+}
+
+@article{rajkomar2018,
+  author  = {Rajkomar, Alvin and Oren, Eyal and Chen, Kai and Dai, Andrew M. and Hajaj, Nissan and Hardt, Michaela and Liu, Peter J. and Liu, Xiaobing and Marcus, Jake and Sun, Mimi and Sundberg, Patrik and Yee, Hector and Zhang, Kun and Zhang, Yi and Flores, Gerardo and Duggan, Gavin E. and Irvine, Jamie and Le, Quoc and Litsch, Kurt and Mossin, Alexander and Tansuwan, Justin and Wang, De and Wexler, James and Wilson, Jimbo and Ludwig, Dana and Volchenboum, Samuel L. and Chou, Katherine and Pearson, Michael and Madabushi, Srinivasan and Shah, Nigam H. and Butte, Atul J. and Howell, Michael D. and Cui, Claire and Corrado, Greg S. and Dean, Jeffrey},
+  title   = {Scalable and accurate deep learning with electronic health records},
+  journal = {npj Digital Medicine},
+  year    = {2018},
+  volume  = {1},
+  pages   = {18}
+}
+
+@article{rudin2019,
+  author  = {Rudin, Cynthia},
+  title   = {Stop Explaining Black Box Machine Learning Models for High Stakes Decisions and Use Interpretable Models Instead},
+  journal = {Nature Machine Intelligence},
+  year    = {2019},
+  volume  = {1},
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+}
+
+@article{hansen2011,
+  author  = {Hansen, Luke O. and Young, Robert S. and Hinami, Keiki and Leung, Albert and Williams, Mark V.},
+  title   = {Interventions to reduce 30-day rehospitalization: a systematic review},
+  journal = {Annals of Internal Medicine},
+  year    = {2011},
+  volume  = {155},
+  number  = {8},
+  pages   = {520--528}
+}
+
+@article{coleman2006,
+  author  = {Coleman, Eric A. and Parry, Carla and Chalmers, Sandra and Min, Sung-joon},
+  title   = {The care transitions intervention: results of a randomized controlled trial},
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+  year    = {2006},
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+  number  = {17},
+  pages   = {1822--1828}
+}
+
+@article{joynt2013,
+  author  = {Joynt, Karen E. and Jha, Ashish K.},
+  title   = {Characteristics of hospitals receiving penalties under the {Hospital Readmissions Reduction Program}},
+  journal = {JAMA},
+  year    = {2013},
+  volume  = {309},
+  number  = {4},
+  pages   = {342--343}
+}
+
+@article{desai2016,
+  author  = {Desai, Nihar R. and Ross, Joseph S. and Kwon, Jin Yul and others},
+  title   = {Association Between Hospital Penalty Status Under the {Hospital Readmission Reduction Program} and Readmission Rates for Target and Nontarget Conditions},
+  journal = {JAMA},
+  year    = {2016},
+  volume  = {316},
+  number  = {24},
+  pages   = {2647--2656}
+}
+
+@article{zuckerman2017,
+  author  = {Zuckerman, Rachael B. and Sheingold, Steven H. and Orav, E. John and Ruhter, Jordan and Epstein, Arnold M.},
+  title   = {Effect of a Hospital-wide Measure on the Readmissions Reduction Program},
+  journal = {New England Journal of Medicine},
+  year    = {2017},
+  volume  = {377},
+  number  = {16},
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+}
+
+@article{obermeyer2019,
+  author  = {Obermeyer, Ziad and Powers, Brian and Vogeli, Christine and Mullainathan, Sendhil},
+  title   = {Dissecting racial bias in an algorithm used to manage the health of populations},
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+}
+
+@article{kind2014,
+  author  = {Kind, Amy J. H. and Jencks, Stephen and Brock, Jim and others},
+  title   = {Neighborhood socioeconomic disadvantage and 30-day rehospitalization: a retrospective cohort study},
+  journal = {Annals of Internal Medicine},
+  year    = {2014},
+  volume  = {161},
+  number  = {11},
+  pages   = {765--774}
+}
+
+@article{joynt2011,
+  author  = {Joynt, Karen E. and Orav, E. John and Jha, Ashish K.},
+  title   = {Thirty-day readmission rates for {Medicare} beneficiaries by race and site of care},
+  journal = {JAMA},
+  year    = {2011},
+  volume  = {305},
+  number  = {7},
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+}
+
+@article{collins2015,
+  author  = {Collins, Gary S. and Reitsma, Johannes B. and Altman, Douglas G. and Moons, Karel G. M.},
+  title   = {Transparent Reporting of a multivariable prediction model for Individual Prognosis or Diagnosis ({TRIPOD}): the {TRIPOD} statement},
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+  year    = {2015},
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+  number  = {1},
+  pages   = {55--63}
+}

levineuwirth.cabal

@@ -20,9 +20,9 @@ executable site
         SimilarLinks
         Compilers
         Contexts
+        Patterns
         Stats
         Stability
-        Metadata
         Tags
         Pagination
         Citations
@@ -33,6 +33,7 @@ executable site
         Filters.Smallcaps
         Filters.Wikilinks
         Filters.Transclusion
+        Filters.EmbedPdf
         Filters.Links
         Filters.Math
         Filters.Code
@@ -56,9 +57,10 @@ executable site
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pyproject.toml

@@ -5,16 +5,19 @@ description = "Build-time tooling for levineuwirth.org"
 requires-python = ">=3.12"
 dependencies = [
     # Visualization
-    "matplotlib>=3.9",
+    "matplotlib>=3.9,<4",
-    "altair>=5.4",
+    "altair>=5.4,<6",
 
     # Embedding pipeline
-    "sentence-transformers>=3.4",
+    # Upper bounds are intentionally generous (next major) but always
-    "faiss-cpu>=1.9",
+    # present so that an unrelated `uv sync` upgrade can't silently pull
-    "numpy>=2.0",
+    # an API-breaking 4.x release. Bump deliberately when validating.
-    "beautifulsoup4>=4.12",
+    "sentence-transformers>=3.4,<4",
+    "faiss-cpu>=1.9,<2",
+    "numpy>=2.0,<3",
+    "beautifulsoup4>=4.12,<5",
     # CPU-only torch — avoids pulling ~3 GB of CUDA libraries
-    "torch>=2.5",
+    "torch>=2.5,<3",
 ]
 
 [[tool.uv.index]]

static/css/base.css

@@ -119,7 +119,9 @@
     --page-padding:    1.5rem;
 
     /* Transitions */
-    --transition-fast: 0.15s ease;
+    --transition-fast:    0.15s ease;
+    --transition-medium:  0.28s ease;
+    --transition-slow:    0.5s  ease;
 
     /* Writing activity heatmap (light mode) */
     --hm-0: #e8e8e4;   /* empty cell */
@@ -127,6 +129,29 @@
     --hm-2: #787874;   /* 500–1999 words */
     --hm-3: #424240;   /* 2000–4999 words */
     --hm-4: #1a1a1a;   /* 5000+ words */
+
+    /* Aliases (introduced for build.css, components.css, and the
+       annotation system, all of which referenced custom properties that
+       were never defined). Browsers silently fall back to the property's
+       initial value when var(--undefined) is used, so without these
+       aliases the build/annotation pages would degrade to default
+       greys/serif fonts.
+
+       Defining them here keeps a single source of truth — change the
+       primitive token (--border-muted, --font-sans, --bg-offset) and
+       every consumer follows. */
+    --rule:        var(--border-muted);
+    --font-ui:     var(--font-sans);
+    --bg-subtle:   var(--bg-offset);
+
+    /* Layout breakpoints — referenced from JS via getComputedStyle and
+       documented here for grep. CSS @media queries cannot use custom
+       properties, so the @media values throughout components.css and
+       layout.css must be kept in lockstep with these. */
+    --bp-phone:    540px;
+    --bp-tablet:   680px;
+    --bp-desktop:  900px;
+    --bp-wide:    1500px;
 }
 
 
@@ -139,14 +164,17 @@
     --bg:              #121212;
     --bg-nav:          #181818;
     --bg-offset:       #1a1a1a;
+    /* --text-faint was previously #6a6660, which yields ~2.8:1 contrast
+       on the #121212 background and fails WCAG AA. Bumped to #8b8680 for
+       a contrast of ~3.5:1, the minimum for non-text UI elements. */
     --text:            #d4d0c8;
     --text-muted:      #8c8881;
-    --text-faint:      #6a6660;
+    --text-faint:      #8b8680;
     --border:          #333333;
     --border-muted:    #444444;
 
     --link:            #d4d0c8;
-    --link-underline:  #6a6660;
+    --link-underline:  #8b8680;
     --link-hover:      #ffffff;
     --link-hover-underline: #ffffff;
     --link-visited:    #a39f98;
@@ -154,6 +182,9 @@
     --selection-bg:    #d4d0c8;
     --selection-text:  #121212;
 
+    /* Aliases — kept in sync with the light-mode definitions above. */
+    --bg-subtle:       var(--bg-offset);
+
     /* Writing activity heatmap (dark mode) */
     --hm-0: #252524;
     --hm-1: #484844;
@@ -170,12 +201,12 @@
         --bg-offset:       #1a1a1a;
         --text:            #d4d0c8;
         --text-muted:      #8c8881;
-        --text-faint:      #6a6660;
+        --text-faint:      #8b8680;
         --border:          #333333;
         --border-muted:    #444444;
 
         --link:            #d4d0c8;
-        --link-underline:  #6a6660;
+        --link-underline:  #8b8680;
         --link-hover:      #ffffff;
         --link-hover-underline: #ffffff;
         --link-visited:    #a39f98;
@@ -183,6 +214,8 @@
         --selection-bg:    #d4d0c8;
         --selection-text:  #121212;
 
+        --bg-subtle:       var(--bg-offset);
+
         --hm-0: #252524;
         --hm-1: #484844;
         --hm-2: #6e6e6a;
@@ -228,6 +261,38 @@ body {
     color: var(--selection-text);
 }
 
+/* Global keyboard-focus indicator. Applies only when the user navigates
+   with the keyboard (`:focus-visible`), not on mouse click, so it does
+   not interfere with normal click feedback. Buttons, anchors, summaries
+   and form controls all share a single 2px outline so the focus path is
+   visible regardless of the surrounding component styling.
+
+   Individual components may override this with a tighter or differently
+   positioned ring, but the default is always present. */
+:focus-visible {
+    outline: 2px solid var(--text);
+    outline-offset: 2px;
+    border-radius: 2px;
+}
+
+button:focus,
+a:focus,
+summary:focus,
+[role="button"]:focus {
+    outline: none;   /* fall back to :focus-visible above */
+}
+
+button:focus-visible,
+a:focus-visible,
+summary:focus-visible,
+[role="button"]:focus-visible,
+input:focus-visible,
+select:focus-visible,
+textarea:focus-visible {
+    outline: 2px solid var(--text);
+    outline-offset: 2px;
+}
+
 img, video, svg {
     max-width: 100%;
     height: auto;

static/css/build.css

@@ -123,6 +123,24 @@
     max-width: 100%;
 }
 
+/* Heatmap intensity classes (driven by CSS vars in base.css) */
+.heatmap-svg .hm0,
+.heatmap-legend .hm0 { fill: var(--hm-0); }
+.heatmap-svg .hm1,
+.heatmap-legend .hm1 { fill: var(--hm-1); }
+.heatmap-svg .hm2,
+.heatmap-legend .hm2 { fill: var(--hm-2); }
+.heatmap-svg .hm3,
+.heatmap-legend .hm3 { fill: var(--hm-3); }
+.heatmap-svg .hm4,
+.heatmap-legend .hm4 { fill: var(--hm-4); }
+
+.heatmap-svg .hm-lbl {
+    font-size: 9px;
+    fill: var(--text-faint);
+    font-family: sans-serif;
+}
+
 /* Legend row below heatmap */
 .heatmap-legend {
     display: flex;

static/css/components.css

@@ -424,7 +424,10 @@ nav.site-nav {
     transform: rotate(-90deg);
 }
 
-/* Nav: animates open/closed via max-height */
+/* Nav: animates open/closed via max-height. The collapsed state hides
+   the nav from the keyboard tab order *and* the accessibility tree
+   using `aria-hidden="true"` (set by toc.js). The transition still
+   works because we keep `max-height: 0` for the visual collapse. */
 .toc-nav {
     overflow: hidden;
     max-height: 80vh;
@@ -432,7 +435,15 @@ nav.site-nav {
 }
 #toc.is-collapsed .toc-nav {
     max-height: 0;
-    visibility: hidden;
+}
+#toc.is-collapsed .toc-nav a,
+#toc.is-collapsed .toc-nav button {
+    /* Belt-and-suspenders: even if aria-hidden is somehow stripped,
+       the collapsed nav cannot receive focus. The earlier rule used
+       `visibility: hidden` which already removed elements from the
+       focus order, but `visibility` interacts poorly with the
+       max-height transition; tabindex=-1 set by toc.js is preferred. */
+    pointer-events: none;
 }
 
 /* Nav list */

static/css/print.css

@@ -5,17 +5,21 @@
 @media print {
 
     /* ----------------------------------------------------------------
-       Force light on paper
+       Force light on paper. The custom-property overrides drive the
+       rest of the cascade — use them consistently below instead of
+       reaching for hardcoded #fff/#000 again.
     ---------------------------------------------------------------- */
     :root,
     [data-theme="dark"] {
         --bg:           #ffffff;
         --bg-offset:    #f5f5f5;
+        --bg-subtle:    #f9f9f9;
         --text:         #000000;
         --text-muted:   #333333;
         --text-faint:   #555555;
         --border:       #cccccc;
         --border-muted: #aaaaaa;
+        --rule:         #cccccc;
     }
 
     /* ----------------------------------------------------------------
@@ -41,8 +45,8 @@
     body {
         font-size: 11pt;
         line-height: 1.6;
-        background: #fff;
+        background: var(--bg);
-        color: #000;
+        color: var(--text);
         margin: 0;
         padding: 0;
     }
@@ -72,9 +76,9 @@
         width: auto !important;
         margin: 0.5em 2em;
         padding: 0.4em 0.8em;
-        border-left: 2px solid #ccc;
+        border-left: 2px solid var(--border);
         font-size: 9pt;
-        color: #555;
+        color: var(--text-faint);
     }
 
     /* ----------------------------------------------------------------
@@ -109,7 +113,7 @@
     a[href^="http"]::after {
         content: " (" attr(href) ")";
         font-size: 0.8em;
-        color: #555;
+        color: var(--text-faint);
         word-break: break-all;
     }
     /* But not for nav or obvious UI links */
@@ -123,8 +127,8 @@
        Code blocks — strip background, border only
     ---------------------------------------------------------------- */
     pre, code {
-        background: #f9f9f9 !important;
+        background: var(--bg-subtle) !important;
-        border: 1px solid #ddd !important;
+        border: 1px solid var(--border-muted) !important;
         box-shadow: none !important;
     }
 
@@ -134,7 +138,7 @@
     .page-meta-footer {
         margin-top: 1.5em;
         padding-top: 1em;
-        border-top: 1px solid #ccc;
+        border-top: 1px solid var(--border);
     }
 
     .meta-footer-full,

static/css/typography.css

@@ -463,9 +463,22 @@ pre code {
     border: 1px solid var(--border-muted); /* Inner bounding box for the image */
 }
 
+/* Image figures: size the box to the image and constrain the caption to the
+   same width. `display: table` + `caption-side: bottom` makes the figure's
+   intrinsic width depend only on its table-cell content (the image), so long
+   captions wrap to the image width instead of stretching the figure off-screen. */
+#markdownBody figure:has(> img) {
+    display: table;
+}
+
+#markdownBody figure:has(> img) > figcaption {
+    display: table-caption;
+    caption-side: bottom;
+}
+
 #markdownBody figcaption {
     font-family: var(--font-sans);
-    font-size: var(--text-size-small);
+    font-size: 0.92em;
     color: var(--text-muted);
     text-align: right; /* Editorial, museum-placard feel */
     margin-top: 1rem;

static/js/annotations.js

@@ -150,12 +150,11 @@
         tooltip.addEventListener('mouseleave', function () { hideTooltip(false); });
     }
 
+    /* Defer to the shared utility (loaded synchronously from
+       templates/partials/head.html) so this file cannot drift from
+       popups.js, semantic-search.js, or build/Utils.hs. */
     function escHtml(s) {
-        return String(s)
+        return window.lnUtils.escapeHtml(s);
-            .replace(/&/g,  '&')
-            .replace(/</g,  '&lt;')
-            .replace(/>/g,  '&gt;')
-            .replace(/"/g,  '&quot;');
     }
 
     function showTooltip(mark, ann) {

static/js/gallery.js

@@ -225,9 +225,37 @@
             if (e.key === 'Escape')     { closeOverlay(); return; }
             if (e.key === 'ArrowLeft')  { navigate(-1);   return; }
             if (e.key === 'ArrowRight') { navigate(+1);   return; }
+            if (e.key === 'Tab')        { trapTab(e);     return; }
         });
     }
 
+    /* Focus trap for the overlay: cycle Tab/Shift+Tab through the
+       focusable controls inside #gallery-overlay so keyboard users
+       cannot tab out into the (currently inert) page background. */
+    function trapTab(e) {
+        var focusable = Array.from(overlay.querySelectorAll(
+            'button:not([disabled]), [tabindex]:not([tabindex="-1"])'
+        ));
+        if (focusable.length === 0) {
+            e.preventDefault();
+            return;
+        }
+        var first = focusable[0];
+        var last  = focusable[focusable.length - 1];
+        var active = document.activeElement;
+        if (e.shiftKey) {
+            if (active === first || !overlay.contains(active)) {
+                e.preventDefault();
+                last.focus();
+            }
+        } else {
+            if (active === last || !overlay.contains(active)) {
+                e.preventDefault();
+                first.focus();
+            }
+        }
+    }
+
     function openOverlay(idx) {
         currentIdx = idx;
         /* Show before rendering — measurements (scrollWidth etc.) return 0

static/js/katex-bootstrap.js

@@ -0,0 +1,40 @@
+/* katex-bootstrap.js — Render every <span class="math"> / <div class="math">
+   block once KaTeX has finished loading.
+
+   Pandoc emits math blocks with the `math` class and the LaTeX source as
+   the element's text content. KaTeX is loaded with `defer` so this
+   bootstrap can simply run on DOMContentLoaded — KaTeX guarantees its
+   own definitions are available by then.
+
+   Used to live as an inline `onload="..."` attribute on the KaTeX
+   <script> tag in templates/default.html, which blocked any future
+   strict CSP. Externalized here so the entire site can run with
+   `script-src 'self'` plus a single CDN allowance.
+*/
+(function () {
+    'use strict';
+
+    function renderAll() {
+        if (typeof katex === 'undefined') return;
+        var nodes = Array.from(document.getElementsByClassName('math'));
+        nodes.forEach(function (el) {
+            if (el.tagName !== 'SPAN' && el.tagName !== 'DIV') return;
+            var src = el.textContent;
+            try {
+                katex.render(src, el, {
+                    displayMode:  el.classList.contains('display'),
+                    output:       'htmlAndMathml',
+                    throwOnError: false
+                });
+            } catch (_) {
+                /* leave the original source visible if KaTeX rejects it */
+            }
+        });
+    }
+
+    if (document.readyState === 'loading') {
+        document.addEventListener('DOMContentLoaded', renderAll);
+    } else {
+        renderAll();
+    }
+})();

static/js/lightbox.js

@@ -15,7 +15,10 @@
 
         var img = document.createElement('img');
         img.className = 'lightbox-img';
-        img.alt = '';
+        /* Default accessible name; overwritten in open() with the
+           triggering image's alt when present. Avoids a nameless
+           lightbox image when the source img has no alt text. */
+        img.alt = 'Lightbox image';
 
         var caption = document.createElement('p');
         caption.className = 'lightbox-caption';
@@ -39,7 +42,10 @@
         function open(src, alt, captionText, trigger) {
             triggerEl = trigger || null;
             img.src = src;
-            img.alt = alt || '';
+            /* Prefer the source img's alt; fall back to the figure
+               caption; fall back to a generic label so the lightbox
+               image always has an accessible name. */
+            img.alt = alt || captionText || 'Lightbox image';
             caption.textContent = captionText || '';
             caption.hidden = !captionText;
             overlay.classList.add('is-open');

static/js/popups.js

@@ -99,6 +99,18 @@
         });
     }
 
+    /* Public re-init hook used by transclude.js after it injects new
+       content into the DOM. Idempotent — bind() marks each element so
+       repeated calls don't stack listeners. */
+    window.reinitPopups = function (container) {
+        if (!popup) return;          /* init() not yet run / touch device */
+        if (annotations === null) {
+            loadAnnotations().then(function () { bindTargets(container || document.body); });
+        } else {
+            bindTargets(container || document.body);
+        }
+    };
+
     /* Returns the appropriate provider function for a given URL, or null. */
     function getProvider(href) {
         if (!href) return null;
@@ -118,6 +130,11 @@
     }
 
     function bind(el, provider) {
+        /* Idempotent: skip elements that already have a popup binding,
+           so reinitPopups() called from transclude.js cannot stack
+           listeners on already-bound nodes. */
+        if (el.dataset.popupBound === '1') return;
+        el.dataset.popupBound = '1';
         el.addEventListener('mouseenter', function () { scheduleShow(el, provider); });
         el.addEventListener('mouseleave', scheduleHide);
         el.addEventListener('focus',      function () { scheduleShow(el, provider); });
@@ -133,9 +150,20 @@
         clearTimeout(showTimer);
         activeTarget = target;
         showTimer = setTimeout(function () {
-            provider(target).then(function (html) {
+            provider(target).then(function (content) {
-                if (!html || activeTarget !== target) return;
+                if (!content || activeTarget !== target) return;
-                popup.innerHTML = html;
+                /* Providers may return either an HTML string or a DOM
+                   Node — the latter is used by epistemicContent so the
+                   popup receives cloned nodes instead of a re-parsed
+                   HTML round-trip. Handle both forms. */
+                popup.innerHTML = '';
+                if (typeof content === 'string') {
+                    popup.innerHTML = content;
+                } else if (content instanceof Node) {
+                    popup.appendChild(content);
+                } else {
+                    return;
+                }
                 positionPopup(target);
                 popup.classList.add('is-visible');
                 popup.setAttribute('aria-hidden', 'false');
@@ -183,6 +211,34 @@
        Content providers
     ------------------------------------------------------------------ */
 
+    /* Cross-origin JSON fetch helper.
+       Validates Content-Type before parsing so a CORS-enabled endpoint
+       cannot return text/html and have it interpreted as JSON. The
+       caller's `.catch` still applies if the JSON parse itself fails.
+
+       Mirror helpers exist for text/* (XML/Atom) and HTML responses. */
+    function fetchJson(url, init) {
+        return fetch(url, init).then(function (r) {
+            if (!r.ok) return null;
+            var ct = (r.headers.get('content-type') || '').toLowerCase();
+            if (ct && !/(?:^|[\s;,])(?:application\/[a-z+.-]*json|text\/json)\b/.test(ct)) {
+                return null;
+            }
+            return r.json();
+        });
+    }
+
+    function fetchXml(url, init) {
+        return fetch(url, init).then(function (r) {
+            if (!r.ok) return null;
+            var ct = (r.headers.get('content-type') || '').toLowerCase();
+            if (ct && !/(?:xml|atom)/.test(ct)) {
+                return null;
+            }
+            return r.text();
+        });
+    }
+
     /* 0. Local annotations — synchronous map lookup after eager load */
     function loadAnnotations() {
         if (annotations !== null) return Promise.resolve(annotations);
@@ -288,8 +344,7 @@
             + '?action=query&prop=extracts&exintro=1&format=json&redirects=1'
             + '&titles=' + encodeURIComponent(decodeURIComponent(m[1])) + '&origin=*';
 
-        return fetch(apiUrl)
+        return fetchJson(apiUrl)
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 var pages = data && data.query && data.query.pages;
                 if (!pages) return null;
@@ -323,8 +378,7 @@
         if (!m) return Promise.resolve(null);
 
         var id = m[1].replace(/v\d+$/, '');
-        return fetch('https://export.arxiv.org/api/query?id_list=' + encodeURIComponent(id))
+        return fetchXml('https://export.arxiv.org/api/query?id_list=' + encodeURIComponent(id))
-            .then(function (r) { return r.ok ? r.text() : null; })
             .then(function (xml) {
                 if (!xml) return null;
                 var doc       = new DOMParser().parseFromString(xml, 'application/xml');
@@ -357,8 +411,7 @@
         var m = href.match(/(?:dx\.)?doi\.org\/(10\.[^?#\s]+)/);
         if (!m) return Promise.resolve(null);
 
-        return fetch('https://api.crossref.org/works/' + encodeURIComponent(m[1]))
+        return fetchJson('https://api.crossref.org/works/' + encodeURIComponent(m[1]))
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 var msg = data && data.message;
                 if (!msg) return null;
@@ -394,9 +447,8 @@
         var m = href.match(/github\.com\/([^/]+)\/([^/?#]+)/);
         if (!m) return Promise.resolve(null);
 
-        return fetch('https://api.github.com/repos/' + m[1] + '/' + m[2],
+        return fetchJson('https://api.github.com/repos/' + m[1] + '/' + m[2],
-                     { headers: { 'Accept': 'application/vnd.github.v3+json' } })
+                         { headers: { 'Accept': 'application/vnd.github.v3+json' } })
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 if (!data || !data.full_name) return null;
                 var meta = [data.language, data.stargazers_count != null ? '\u2605\u00a0' + data.stargazers_count : null]
@@ -421,8 +473,7 @@
         if (!m) return Promise.resolve(null);
 
         var apiUrl = 'https://git.levineuwirth.org/api/v1/repos/' + m[1] + '/' + m[2];
-        return fetch(apiUrl)
+        return fetchJson(apiUrl)
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 if (!data || !data.full_name) return null;
                 var meta = [data.language, data.stars_count != null ? '\u2605\u00a0' + data.stars_count : null]
@@ -446,8 +497,7 @@
         var base   = href.replace(/[?#].*$/, '');
         var apiUrl = base + '.json';
 
-        return fetch(apiUrl)
+        return fetchJson(apiUrl)
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 if (!data || !data.title) return null;
                 var desc = data.description;
@@ -476,8 +526,7 @@
         var server = /medrxiv/.test(href) ? 'medrxiv' : 'biorxiv';
         var label  = server === 'medrxiv' ? 'medRxiv' : 'bioRxiv';
 
-        return fetch('https://api.biorxiv.org/details/' + server + '/' + encodeURIComponent(doi) + '/json')
+        return fetchJson('https://api.biorxiv.org/details/' + server + '/' + encodeURIComponent(doi) + '/json')
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 var paper = data && data.collection && data.collection[0];
                 if (!paper || !paper.title) return null;
@@ -505,8 +554,7 @@
         var href = target.getAttribute('href');
         if (!href || cache[href]) return Promise.resolve(cache[href] || null);
 
-        return fetch('https://www.youtube.com/oembed?url=' + encodeURIComponent(href) + '&format=json')
+        return fetchJson('https://www.youtube.com/oembed?url=' + encodeURIComponent(href) + '&format=json')
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 if (!data || !data.title) return null;
                 return store(href,
@@ -527,8 +575,7 @@
         var m = href.match(/archive\.org\/details\/([^/?#]+)/);
         if (!m) return Promise.resolve(null);
 
-        return fetch('https://archive.org/metadata/' + encodeURIComponent(m[1]))
+        return fetchJson('https://archive.org/metadata/' + encodeURIComponent(m[1]))
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 var meta = data && data.metadata;
                 if (!meta) return null;
@@ -564,8 +611,7 @@
         var apiUrl = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi'
                    + '?db=pubmed&id=' + pmid + '&retmode=json';
 
-        return fetch(apiUrl)
+        return fetchJson(apiUrl)
-            .then(function (r) { return r.ok ? r.json() : null; })
             .then(function (data) {
                 var paper = data && data.result && data.result[pmid];
                 if (!paper || !paper.title) return null;
@@ -597,25 +643,34 @@
 
     /* Epistemic jump link — reads the #epistemic section already in the DOM
        and renders a compact summary: status/confidence/dots + expanded DL.
-       All ep-* classes are already styled via components.css. */
+       All ep-* classes are already styled via components.css.
+
+       Returns a DocumentFragment instead of an HTML string so the popup
+       receives cloned nodes (defense in depth — if a future change ever
+       allowed user-authored HTML into the source section, the popup
+       would still see exactly the same already-rendered DOM rather than
+       a re-parsed string). */
     function epistemicContent() {
         var section = document.getElementById('epistemic');
         if (!section) return Promise.resolve(null);
 
-        var html = '<div class="popup-epistemic">';
+        var wrap = document.createElement('div');
+        wrap.className = 'popup-epistemic';
 
         var compact = section.querySelector('.ep-compact');
         if (compact) {
-            html += '<div class="ep-compact">' + compact.innerHTML + '</div>';
+            var compactClone = compact.cloneNode(true);
+            wrap.appendChild(compactClone);
         }
 
         var expanded = section.querySelector('.ep-expanded');
         if (expanded) {
-            html += '<dl class="ep-expanded">' + expanded.innerHTML + '</dl>';
+            var expandedClone = expanded.cloneNode(true);
+            wrap.appendChild(expandedClone);
         }
 
-        html += '</div>';
+        if (!compact && !expanded) return Promise.resolve(null);
-        return Promise.resolve(html || null);
+        return Promise.resolve(wrap);
     }
 
     /* Local PDF — shows the build-time first-page thumbnail (.thumb.png).
@@ -652,12 +707,11 @@
             });
     }
 
+    /* Defer to the shared utility (loaded synchronously from
+       templates/partials/head.html) so this file cannot drift from
+       annotations.js, semantic-search.js, or build/Utils.hs. */
     function esc(s) {
-        return String(s)
+        return window.lnUtils.escapeHtml(s);
-            .replace(/&/g, '&amp;')
-            .replace(/</g, '&lt;')
-            .replace(/>/g, '&gt;')
-            .replace(/"/g, '&quot;');
     }
 
     /* Emit a .popup-source label with a data-popup-source attribute so CSS

static/js/semantic-search.js

@@ -62,10 +62,17 @@
        Model loading — dynamic import from CDN, lazy
     ------------------------------------------------------------------ */
 
+    /* In-flight promise so concurrent searches share a single model
+       load. Without this guard, two rapid keystrokes would each call
+       `import(CDN)` and `pipeline(...)`, wasting CPU and memory before
+       the second resolves. */
+    var loadModelPromise = null;
+
     function loadModel() {
         if (extractor) return Promise.resolve(extractor);
+        if (loadModelPromise) return loadModelPromise;
         setStatus('Loading model…');
-        return import(CDN).then(function (mod) {
+        loadModelPromise = import(CDN).then(function (mod) {
             /* Point transformers.js at our self-hosted model files. */
             mod.env.localModelPath   = MODEL_PATH;
             mod.env.allowRemoteModels = false;
@@ -73,7 +80,13 @@
         }).then(function (pipe) {
             extractor = pipe;
             return extractor;
+        }).catch(function (err) {
+            /* Allow a retry on the next call instead of caching the
+               failed promise forever. */
+            loadModelPromise = null;
+            throw err;
         });
+        return loadModelPromise;
     }
 
     /* ------------------------------------------------------------------
@@ -163,12 +176,11 @@
         statusEl.textContent = msg;
     }
 
+    /* Defer to the shared utility (loaded synchronously from
+       templates/partials/head.html) so this file cannot drift from
+       popups.js, annotations.js, or build/Utils.hs. */
     function esc(s) {
-        return String(s)
+        return window.lnUtils.escapeHtml(s);
-            .replace(/&/g, '&')
-            .replace(/</g, '&lt;')
-            .replace(/>/g, '&gt;')
-            .replace(/"/g, '&quot;');
     }
 
     /* ------------------------------------------------------------------

static/js/settings.js

@@ -1,11 +1,19 @@
 /* settings.js — Settings panel: theme, text size, print.
-   Must stay in sync with TEXT_SIZES in theme.js. */
+   Must stay in sync with TEXT_SIZES in theme.js.
+
+   All localStorage access routes through window.lnUtils.safeStorage so
+   Safari private-mode SecurityErrors on writes do not throw uncaught. */
 (function () {
     'use strict';
 
     var TEXT_SIZES    = [20, 23, 26];
     var TEXT_SIZE_DEFAULT = 1;      /* index of 23px */
     var TEXT_SIZE_KEY = 'text-size';
+    var store = (window.lnUtils && window.lnUtils.safeStorage) || {
+        get: function () { return null; },
+        set: function () { return false; },
+        remove: function () { return false; }
+    };
 
     /* ------------------------------------------------------------------
        Init
@@ -102,7 +110,7 @@
 
     function setTheme(theme) {
         document.documentElement.setAttribute('data-theme', theme);
-        localStorage.setItem('theme', theme);
+        store.set('theme', theme);
         syncThemeButtons();
     }
 
@@ -122,13 +130,13 @@
     /* Text size ------------------------------------------------------- */
 
     function getSizeIndex() {
-        var n = parseInt(localStorage.getItem(TEXT_SIZE_KEY), 10);
+        var n = parseInt(store.get(TEXT_SIZE_KEY), 10);
         return (isNaN(n) || n < 0 || n >= TEXT_SIZES.length) ? TEXT_SIZE_DEFAULT : n;
     }
 
     function shiftSize(delta) {
         var idx = Math.max(0, Math.min(TEXT_SIZES.length - 1, getSizeIndex() + delta));
-        localStorage.setItem(TEXT_SIZE_KEY, idx);
+        store.set(TEXT_SIZE_KEY, idx);
         document.documentElement.style.setProperty('--text-size', TEXT_SIZES[idx] + 'px');
         syncTextSizeButtons();
     }
@@ -140,10 +148,10 @@
         var on   = html.hasAttribute(attrName);
         if (on) {
             html.removeAttribute(attrName);
-            localStorage.removeItem(storageKey);
+            store.remove(storageKey);
         } else {
             html.setAttribute(attrName, '');
-            localStorage.setItem(storageKey, '1');
+            store.set(storageKey, '1');
         }
         syncToggleButton(storageKey, attrName);
     }

static/js/sidenotes.js

@@ -52,13 +52,19 @@
     }
 
     /* ------------------------------------------------------------------ */
-    /*  Hover + click wiring                                               */
+    /*  Hover + click + keyboard wiring                                    */
     /* ------------------------------------------------------------------ */
 
     /* At most one sidenote is "focused" (click-sticky) at a time. */
     let focusedPair = null;
 
     function wireHover(ref, sn) {
+        /* Idempotent: skip pairs already wired so 'reinitSidenotes'
+           after a transclusion injection cannot stack listeners. */
+        if (ref.dataset.snBound === '1') return;
+        ref.dataset.snBound = '1';
+        sn.dataset.snBound  = '1';
+
         let hovering = false;
         let focused  = false;
 
@@ -70,6 +76,22 @@
 
         function unfocus() { focused = false; update(); }
 
+        function toggleFocus() {
+            /* Sticky focus only makes sense on wide viewports where the
+               sidenote is actually visible. On narrow screens there's
+               nothing to pin. */
+            if (getComputedStyle(sn).display === 'none') return;
+            if (focused) {
+                focused = false;
+                focusedPair = null;
+            } else {
+                if (focusedPair) focusedPair.unfocus();
+                focused = true;
+                focusedPair = { ref: ref, sn: sn, unfocus: unfocus };
+            }
+            update();
+        }
+
         ref.addEventListener('mouseenter', function () { hovering = true;  update(); });
         ref.addEventListener('mouseleave', function () { hovering = false; update(); });
         sn.addEventListener('mouseenter',  function () { hovering = true;  update(); });
@@ -81,16 +103,25 @@
         if (link) {
             link.addEventListener('click', function (e) {
                 e.preventDefault();
-                if (getComputedStyle(sn).display === 'none') return; /* narrow: no sidenote to focus */
+                toggleFocus();
-                if (focused) {
+            });
+
+            /* Keyboard activation: Enter follows the link by default (the
+               browser synthesizes a click), but Space does not. Both are
+               expected to toggle focus on a focus-activated element, so
+               we normalize: Enter/Space toggle, Escape clears if focused.
+               The <a href="#sn-N"> retains its native focusability so
+               Tab reaches it; we only intercept the key. */
+            link.addEventListener('keydown', function (e) {
+                if (e.key === ' ') {
+                    e.preventDefault();
+                    toggleFocus();
+                } else if (e.key === 'Escape' && focused) {
+                    e.preventDefault();
                     focused = false;
                     focusedPair = null;
-                } else {
+                    update();
-                    if (focusedPair) focusedPair.unfocus();
-                    focused = true;
-                    focusedPair = { ref: ref, sn: sn, unfocus: unfocus };
                 }
-                update();
             });
         }
     }
@@ -105,19 +136,39 @@
         }
     });
 
-    function init() {
+    /* Global Escape dismisses any sticky-focused sidenote, even if focus
-        const body = document.getElementById('markdownBody');
+       has moved away from the ref link. */
-        if (!body) return;
+    document.addEventListener('keydown', function (e) {
+        if (e.key === 'Escape' && focusedPair) {
+            focusedPair.unfocus();
+            focusedPair = null;
+        }
+    });
 
-        body.querySelectorAll('.sidenote').forEach(function (sn) {
+    function wireAll(root) {
+        root.querySelectorAll('.sidenote').forEach(function (sn) {
             const refId = 'snref-' + sn.id.slice(3);
             const ref   = document.getElementById(refId);
             if (ref) wireHover(ref, sn);
         });
+    }
 
+    function init() {
+        const body = document.getElementById('markdownBody');
+        if (!body) return;
+
+        wireAll(body);
         positionSidenotes();
     }
 
+    /* Public re-init hook used by transclude.js after it injects new
+       content. wireAll is idempotent so calling this multiple times is
+       safe. */
+    window.reinitSidenotes = function (container) {
+        wireAll(container || document.getElementById('markdownBody') || document);
+        positionSidenotes();
+    };
+
     document.addEventListener('DOMContentLoaded', init);
     window.addEventListener('resize', positionSidenotes);
 }());

static/js/theme.js

@@ -1,29 +1,36 @@
 /* theme.js — Restores theme and text size from localStorage before first paint.
    Loaded synchronously (no defer/async) to prevent flash of wrong appearance.
    DOM interaction (button wiring) is handled by settings.js (deferred).
+
+   All storage access routes through window.lnUtils.safeStorage (from
+   utils.js, loaded immediately before this script) so Safari private-mode
+   SecurityErrors degrade to default appearance rather than blowing up
+   the synchronous bootstrap.
 */
 (function () {
     var TEXT_SIZES = [20, 23, 26];
+    var store = window.lnUtils && window.lnUtils.safeStorage;
+    function safeGet(key) { return store ? store.get(key) : null; }
 
     /* Theme */
-    var storedTheme = localStorage.getItem('theme');
+    var storedTheme = safeGet('theme');
     if (storedTheme === 'dark' || storedTheme === 'light') {
         document.documentElement.setAttribute('data-theme', storedTheme);
     }
 
     /* Text size */
-    var storedSize = parseInt(localStorage.getItem('text-size'), 10);
+    var storedSize = parseInt(safeGet('text-size'), 10);
     if (!isNaN(storedSize) && storedSize >= 0 && storedSize < TEXT_SIZES.length) {
         document.documentElement.style.setProperty('--text-size', TEXT_SIZES[storedSize] + 'px');
     }
 
     /* Focus mode */
-    if (localStorage.getItem('focus-mode')) {
+    if (safeGet('focus-mode')) {
         document.documentElement.setAttribute('data-focus-mode', '');
     }
 
     /* Reduce motion */
-    if (localStorage.getItem('reduce-motion')) {
+    if (safeGet('reduce-motion')) {
         document.documentElement.setAttribute('data-reduce-motion', '');
     }
 })();

static/js/toc.js

@@ -39,11 +39,26 @@
             }
         }
 
-        // Collapse / expand
+        // Collapse / expand. The collapsed state is hidden from
+        // assistive technology (aria-hidden="true") and removed from
+        // the keyboard tab order (tabindex=-1 on each link), so users
+        // navigating with a screen reader or only the keyboard cannot
+        // land on links inside a collapsed TOC.
+        const tocNav = toc.querySelector('.toc-nav');
         function setExpanded(open) {
             if (!toggleBtn) return;
             toc.classList.toggle('is-collapsed', !open);
             toggleBtn.setAttribute('aria-expanded', String(open));
+            if (tocNav) {
+                tocNav.setAttribute('aria-hidden', String(!open));
+            }
+            links.forEach(function (a) {
+                if (open) {
+                    a.removeAttribute('tabindex');
+                } else {
+                    a.setAttribute('tabindex', '-1');
+                }
+            });
         }
 
         setExpanded(true);
@@ -54,13 +69,6 @@
             });
         }
 
-        // Auto-collapse once the first section becomes active via scrolling.
-        let autoCollapsed = false;
-        function collapseOnce() {
-            if (autoCollapsed) return;
-            autoCollapsed = true;
-            setExpanded(false);
-        }
 
         // Progress indicator — drives the horizontal bar under .toc-header.
         function updateProgress() {
@@ -83,7 +91,7 @@
             if (visible.size > 0) {
                 // Activate the topmost visible heading in document order.
                 const top = headings.find(h => visible.has(h));
-                if (top) { activate(top.id); collapseOnce(); }
+                if (top) { activate(top.id); }
             } else {
                 // Nothing in the trigger band: activate the last heading
                 // whose top edge is above the sticky nav bar.
@@ -93,7 +101,7 @@
                     if (h.getBoundingClientRect().top < navHeight + 16) candidate = h;
                     else break;
                 }
-                if (candidate) { activate(candidate.id); collapseOnce(); }
+                if (candidate) { activate(candidate.id); }
                 else activateTitle();
             }
         }, {

static/js/transclude.js

@@ -81,8 +81,21 @@
 
     /* After injection, retrigger layout-dependent subsystems. */
     function reinitFragment(container) {
-        /* sidenotes.js repositions on resize — dispatch to trigger it. */
+        /* sidenotes.js — wire newly injected sidenote refs/spans and
-        window.dispatchEvent(new Event('resize'));
+           reposition the column. Falls back to a manual resize event
+           for older builds that haven't been redeployed yet. */
+        if (typeof window.reinitSidenotes === 'function') {
+            window.reinitSidenotes(container);
+        } else {
+            window.dispatchEvent(new Event('resize'));
+        }
+
+        /* popups.js — bind hover popups for newly injected links so
+           transcluded content has the same preview behaviour as the
+           host page. */
+        if (typeof window.reinitPopups === 'function') {
+            window.reinitPopups(container);
+        }
 
         /* collapse.js exposes reinitCollapse for newly added headings. */
         if (typeof window.reinitCollapse === 'function') {

static/js/utils.js

@@ -0,0 +1,48 @@
+/* utils.js — Tiny shared helpers loaded before any other script.
+   Loaded synchronously (no `defer`) from templates/partials/head.html so
+   that defer'd scripts can rely on `window.lnUtils` existing at run time.
+
+   Keep this file dependency-free and minimal. It's the lowest-level
+   layer in the JS stack — anything heavier should live in a feature
+   module instead. */
+(function (global) {
+    'use strict';
+
+    var lnUtils = global.lnUtils || {};
+
+    /* Escape a string for safe interpolation into HTML text content or
+       double-quoted attribute values. The order of replacements matters:
+       `&` MUST come first, otherwise the `&` injected by other rules
+       gets re-escaped to `&`.
+
+       Mirror of `Utils.escapeHtml` in build/Utils.hs. */
+    lnUtils.escapeHtml = function (s) {
+        return String(s)
+            .replace(/&/g,  '&')
+            .replace(/</g,  '&lt;')
+            .replace(/>/g,  '&gt;')
+            .replace(/"/g,  '&quot;')
+            .replace(/'/g,  '&#39;');
+    };
+
+    /* Safe localStorage wrapper. Safari throws SecurityError in private
+       browsing mode on every access — including writes — so reads AND
+       writes need to be guarded. Every consumer that touches storage
+       should route through this helper so degradation is uniform. */
+    lnUtils.safeStorage = {
+        get: function (key) {
+            try { return localStorage.getItem(key); }
+            catch (_) { return null; }
+        },
+        set: function (key, value) {
+            try { localStorage.setItem(key, value); return true; }
+            catch (_) { return false; }
+        },
+        remove: function (key) {
+            try { localStorage.removeItem(key); return true; }
+            catch (_) { return false; }
+        }
+    };
+
+    global.lnUtils = lnUtils;
+})(window);

templates/default.html

@@ -28,8 +28,8 @@ $if(home)$<script src="/js/random.js" defer></script>$endif$
 $if(reading)$<script src="/js/reading.js" defer></script>$endif$
 $for(page-scripts)$<script src="/$script-src$" defer></script>$endfor$
 $if(math)$
-<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js"
+<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js"></script>
-    onload="(function(){var els=Array.from(document.getElementsByClassName('math'));els.forEach(function(el){if(el.tagName==='SPAN'){var src=el.textContent;katex.render(src,el,{displayMode:el.classList.contains('display'),output:'htmlAndMathml',throwOnError:false})}})})()"></script>
+<script defer src="/js/katex-bootstrap.js"></script>
 $endif$
 </body>
 </html>

templates/partials/head.html

@@ -28,6 +28,7 @@ $endif$
 $if(search)$
 <link rel="stylesheet" href="/pagefind/pagefind-ui.css">
 $endif$
+<script src="/js/utils.js"></script>
 <script src="/js/theme.js"></script>
 $if(viz)$
 <link rel="stylesheet" href="/css/viz.css">

templates/partials/nav.html

@@ -12,36 +12,36 @@
                 <a href="/search.html">Search</a>
             </div>
             <div class="nav-controls">
-                <button class="nav-portal-toggle" aria-label="Toggle portals" aria-expanded="false">
+                <button type="button" class="nav-portal-toggle" aria-label="Toggle portals" aria-expanded="false">
                     <span class="nav-portal-arrow">▼</span>Portals
                 </button>
                 <div class="settings-wrap">
-                    <button class="settings-toggle" aria-label="Open settings" aria-expanded="false">⚙</button>
+                    <button type="button" class="settings-toggle" aria-label="Open settings" aria-expanded="false">⚙</button>
                     <div class="settings-panel" aria-hidden="true">
                         <div class="settings-section">
                             <div class="settings-label">Theme</div>
                             <div class="settings-row">
-                                <button class="settings-btn" data-action="theme-light">Light</button>
+                                <button type="button" class="settings-btn" data-action="theme-light">Light</button>
-                                <button class="settings-btn" data-action="theme-dark">Dark</button>
+                                <button type="button" class="settings-btn" data-action="theme-dark">Dark</button>
                             </div>
                         </div>
                         <div class="settings-section">
                             <div class="settings-label">Text size</div>
                             <div class="settings-row">
-                                <button class="settings-btn" data-action="text-smaller" aria-label="Decrease text size">A−</button>
+                                <button type="button" class="settings-btn" data-action="text-smaller" aria-label="Decrease text size">A−</button>
-                                <button class="settings-btn" data-action="text-larger"  aria-label="Increase text size">A+</button>
+                                <button type="button" class="settings-btn" data-action="text-larger"  aria-label="Increase text size">A+</button>
                             </div>
                         </div>
                         <div class="settings-section">
                             <div class="settings-label">Display</div>
                             <div class="settings-col">
-                                <button class="settings-btn settings-btn--full" data-action="focus-mode">Focus Mode</button>
+                                <button type="button" class="settings-btn settings-btn--full" data-action="focus-mode">Focus Mode</button>
-                                <button class="settings-btn settings-btn--full" data-action="reduce-motion">Reduce Motion</button>
+                                <button type="button" class="settings-btn settings-btn--full" data-action="reduce-motion">Reduce Motion</button>
                             </div>
                         </div>
                         <div class="settings-section">
-                            <button class="settings-btn settings-btn--full" data-action="print">Print</button>
+                            <button type="button" class="settings-btn settings-btn--full" data-action="print">Print</button>
-                            <button class="settings-btn settings-btn--full settings-btn--danger" data-action="clear-annotations">Clear Annotations</button>
+                            <button type="button" class="settings-btn settings-btn--full settings-btn--danger" data-action="clear-annotations">Clear Annotations</button>
                         </div>
                     </div>
                 </div>

tools/convert-images.sh

@@ -25,7 +25,7 @@ skipped=0
 
 while IFS= read -r -d '' img; do
     webp="${img%.*}.webp"
-    if [ -f "$webp" ]; then
+    if [ -f "$webp" ] && [ ! "$img" -nt "$webp" ]; then
         skipped=$((skipped + 1))
     else
         echo "  webp  ${img#"$REPO_ROOT/"}"

tools/download-model.sh

@@ -7,25 +7,76 @@
 #
 # Run once before deploying. Files are gitignored (binary artifacts).
 # Re-running is safe — existing files are skipped.
+#
+# Supply chain hardening: each downloaded file is verified against
+# tools/model-checksums.sha256 if that file is present. The checksums
+# file is committed to git so a HuggingFace compromise (or a
+# transparently rebuilt model) cannot silently land in the deployed
+# site. To pin a new model version, run `tools/download-model.sh`,
+# verify the model out-of-band, then commit the generated checksums:
+#
+#     (cd static/models/all-MiniLM-L6-v2 && \
+#      sha256sum config.json tokenizer.json tokenizer_config.json \
+#                special_tokens_map.json onnx/model_quantized.onnx) \
+#      > tools/model-checksums.sha256
 
 set -euo pipefail
 
 REPO_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
 MODEL_DIR="$REPO_ROOT/static/models/all-MiniLM-L6-v2"
 BASE_URL="https://huggingface.co/Xenova/all-MiniLM-L6-v2/resolve/main"
+CHECKSUMS="$REPO_ROOT/tools/model-checksums.sha256"
 
 mkdir -p "$MODEL_DIR/onnx"
 
+# Look up the expected SHA-256 for a relative path, or empty string if
+# no checksums file is present (or the path isn't pinned yet).
+expected_sha() {
+    local rel="$1"
+    if [ ! -f "$CHECKSUMS" ]; then
+        echo ""
+        return
+    fi
+    # Match lines of the form "<sha>  <relative-path>"
+    awk -v p="$rel" '$2 == p { print $1; exit }' "$CHECKSUMS"
+}
+
+verify_sha() {
+    local rel="$1" dst="$2"
+    local want
+    want=$(expected_sha "$rel")
+    if [ -z "$want" ]; then
+        return
+    fi
+    local got
+    got=$(sha256sum "$dst" | awk '{ print $1 }')
+    if [ "$got" != "$want" ]; then
+        echo "  ERROR sha256 mismatch for $rel" >&2
+        echo "        expected $want" >&2
+        echo "        got      $got" >&2
+        rm -f "$dst"
+        exit 1
+    fi
+    echo "  ok    sha256 verified for $rel"
+}
+
 fetch() {
     local src="$1" dst="$2"
     if [ -f "$dst" ]; then
         echo "  skip  $src (already present)"
+        verify_sha "$src" "$dst"
         return
     fi
     echo "  fetch $src"
     curl -fsSL --progress-bar "$BASE_URL/$src" -o "$dst"
+    verify_sha "$src" "$dst"
 }
 
+if [ ! -f "$CHECKSUMS" ]; then
+    echo "Note: $CHECKSUMS not found — downloads will not be SHA-verified." >&2
+    echo "      See the comment in tools/download-model.sh to pin checksums." >&2
+fi
+
 echo "Downloading all-MiniLM-L6-v2 to $MODEL_DIR ..."
 
 fetch "config.json"                  "$MODEL_DIR/config.json"

tools/embed.py

@@ -68,8 +68,10 @@ def needs_update() -> bool:
 def _url_from_path(html_path: Path) -> str:
     rel = html_path.relative_to(SITE_DIR)
     if rel.name == "index.html":
-        url = "/" + str(rel.parent) + "/"
+        parent = str(rel.parent)
-        return url.replace("//", "/")
+        if parent in (".", ""):
+            return "/"
+        return "/" + parent + "/"
     return "/" + str(rel)
 
 def _clean_soup(soup: BeautifulSoup) -> None:

tools/import-poetry.py

@@ -44,9 +44,11 @@ _ROMAN_VALS = [
 
 def roman_to_int(s: str) -> Optional[int]:
     s = s.upper().strip()
+    if not s:
+        return None
     i, result = 0, 0
     for numeral, value in _ROMAN_VALS:
-        while s[i : i + len(numeral)] == numeral:
+        while i < len(s) and s[i : i + len(numeral)] == numeral:
             result += value
             i += len(numeral)
     return result if i == len(s) and result > 0 else None
@@ -191,15 +193,28 @@ def first_content_line(lines: list[str]) -> str:
 # ---------------------------------------------------------------------------
 
 def yaml_str(s: str) -> str:
-    """Quote a string for YAML if it needs it."""
+    """Quote a string for YAML if it needs it.
+
+    Always quote (and escape) when the string contains characters that
+    can break YAML parsing — including newlines, carriage returns, and
+    YAML's reserved indicators. Newlines and carriage returns are escaped
+    using YAML's double-quoted backslash escapes.
+    """
     needs_quote = (
         not s
         or s[0] in " \t"
         or s[-1] in " \t"
-        or any(c in s for c in ':{}[]|>&*!,#?@`\'"')
+        or any(c in s for c in ':{}[]|>&*!,#?@`\'"\n\r\t')
     )
     if needs_quote:
-        return '"' + s.replace("\\", "\\\\").replace('"', '\\"') + '"'
+        escaped = (
+            s.replace("\\", "\\\\")
+             .replace('"', '\\"')
+             .replace("\n", "\\n")
+             .replace("\r", "\\r")
+             .replace("\t", "\\t")
+        )
+        return '"' + escaped + '"'
     return s
 
 # ---------------------------------------------------------------------------
@@ -324,9 +339,39 @@ def main() -> None:
         print(f"error: file not found: {source}", file=sys.stderr)
         sys.exit(1)
 
+    # Validate publication year — flows into YAML unchanged so it must be
+    # well-formed and within a sane range.
+    try:
+        year = int(args.date)
+    except ValueError:
+        print(
+            f"error: --date must be an integer year, got {args.date!r}",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+    if not (1 <= year <= 2100):
+        print(
+            f"error: --date {year} out of plausible range (1..2100)",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+
     # Defaults
     title_prefix     = args.title_prefix or args.collection.rstrip("s")
+    if not title_prefix.strip():
+        print(
+            "error: title prefix is empty (check --title-prefix or --collection)",
+            file=sys.stderr,
+        )
+        sys.exit(1)
     collection_slug  = args.slug or slugify(f"{args.poet}-{args.collection}")
+    if not collection_slug or collection_slug == "-":
+        print(
+            f"error: collection slug is empty "
+            f"(check --slug, --collection={args.collection!r}, --poet={args.poet!r})",
+            file=sys.stderr,
+        )
+        sys.exit(1)
     tags             = [t.strip() for t in args.tags.split(",")]
     out_dir          = POETRY_DIR / collection_slug
 
@@ -389,7 +434,7 @@ def main() -> None:
             print(f"  skip  {path.name}")
             skipped += 1
         else:
-            path.write_text(content, encoding="utf-8")
+            path.write_text(content, encoding="utf-8", errors="strict")
             print(f"  write {path.name}")
             written += 1
 

tools/sign-site.sh

@@ -40,18 +40,15 @@ if ! GNUPGHOME="$GNUPGHOME" gpg \
 fi
 echo "sign-site: pre-flight OK — signing $SITE_DIR..." >&2
 
-count=0
+find "$SITE_DIR" -name "*.html" -print0 | xargs -0 -I {} -P $(nproc) \
-while IFS= read -r -d '' html; do
+    gpg --homedir "$GNUPGHOME" \
-    GNUPGHOME="$GNUPGHOME" gpg \
-        --homedir "$GNUPGHOME" \
         --batch \
         --yes \
         --detach-sign \
         --armor \
         --local-user "$SIGNING_KEY" \
-        --output "${html}.sig" \
+        --output "{}.sig" \
-        "$html"
+        "{}"
-    count=$((count + 1))
-done < <(find "$SITE_DIR" -name "*.html" -print0)
 
+count=$(find "$SITE_DIR" -name "*.html" -printf '.' | wc -c)
 echo "Signed $count HTML files in $SITE_DIR."

uv.lock

@@ -8,40 +8,18 @@ resolution-markers = [
 
 [[package]]
 name = "altair"
-version = "6.0.0"
+version = "5.5.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "jinja2" },
     { name = "jsonschema" },
     { name = "narwhals" },
     { name = "packaging" },
-    { name = "typing-extensions", marker = "python_full_version < '3.15'" },
+    { name = "typing-extensions", marker = "python_full_version < '3.14'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/f7/c0/184a89bd5feba14ff3c41cfaf1dd8a82c05f5ceedbc92145e17042eb08a4/altair-6.0.0.tar.gz", hash = "sha256:614bf5ecbe2337347b590afb111929aa9c16c9527c4887d96c9bc7f6640756b4", size = 763834, upload-time = "2025-11-12T08:59:11.519Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/16/b1/f2969c7bdb8ad8bbdda031687defdce2c19afba2aa2c8e1d2a17f78376d8/altair-5.5.0.tar.gz", hash = "sha256:d960ebe6178c56de3855a68c47b516be38640b73fb3b5111c2a9ca90546dd73d", size = 705305, upload-time = "2024-11-23T23:39:58.542Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/db/33/ef2f2409450ef6daa61459d5de5c08128e7d3edb773fefd0a324d1310238/altair-6.0.0-py3-none-any.whl", hash = "sha256:09ae95b53d5fe5b16987dccc785a7af8588f2dca50de1e7a156efa8a461515f8", size = 795410, upload-time = "2025-11-12T08:59:09.804Z" },
+    { url = "https://files.pythonhosted.org/packages/aa/f3/0b6ced594e51cc95d8c1fc1640d3623770d01e4969d29c0bd09945fafefa/altair-5.5.0-py3-none-any.whl", hash = "sha256:91a310b926508d560fe0148d02a194f38b824122641ef528113d029fcd129f8c", size = 731200, upload-time = "2024-11-23T23:39:56.4Z" },
-]
-
-[[package]]
-name = "annotated-doc"
-version = "0.0.4"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/57/ba/046ceea27344560984e26a590f90bc7f4a75b06701f653222458922b558c/annotated_doc-0.0.4.tar.gz", hash = "sha256:fbcda96e87e9c92ad167c2e53839e57503ecfda18804ea28102353485033faa4", size = 7288, upload-time = "2025-11-10T22:07:42.062Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/1e/d3/26bf1008eb3d2daa8ef4cacc7f3bfdc11818d111f7e2d0201bc6e3b49d45/annotated_doc-0.0.4-py3-none-any.whl", hash = "sha256:571ac1dc6991c450b25a9c2d84a3705e2ae7a53467b5d111c24fa8baabbed320", size = 5303, upload-time = "2025-11-10T22:07:40.673Z" },
-]
-
-[[package]]
-name = "anyio"
-version = "4.12.1"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "idna" },
-    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/96/f0/5eb65b2bb0d09ac6776f2eb54adee6abe8228ea05b20a5ad0e4945de8aac/anyio-4.12.1.tar.gz", hash = "sha256:41cfcc3a4c85d3f05c932da7c26d0201ac36f72abd4435ba90d0464a3ffed703", size = 228685, upload-time = "2026-01-06T11:45:21.246Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/38/0e/27be9fdef66e72d64c0cdc3cc2823101b80585f8119b5c112c2e8f5f7dab/anyio-4.12.1-py3-none-any.whl", hash = "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c", size = 113592, upload-time = "2026-01-06T11:45:19.497Z" },
 ]
 
 [[package]]
@@ -76,15 +54,76 @@ wheels = [
 ]
 
 [[package]]
-name = "click"
+name = "charset-normalizer"
-version = "8.3.1"
+version = "3.4.7"
 source = { registry = "https://pypi.org/simple" }
-dependencies = [
+sdist = { url = "https://files.pythonhosted.org/packages/e7/a1/67fe25fac3c7642725500a3f6cfe5821ad557c3abb11c9d20d12c7008d3e/charset_normalizer-3.4.7.tar.gz", hash = "sha256:ae89db9e5f98a11a4bf50407d4363e7b09b31e55bc117b4f7d80aab97ba009e5", size = 144271, upload-time = "2026-04-02T09:28:39.342Z" }
-    { name = "colorama", marker = "sys_platform == 'win32'" },
-]
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