feat(install): serve several sources instead of displacing them

~/.agents/skills was a single link straight at this checkout. That encoded an
assumption nobody had stated — that this checkout is the only source of skills
on the host. On flamingo it was not: Crush's directory held Anthropic's
official set, and the only way to install this library was to move that set
aside. A capability loss dressed up as a tidy-up.

The canonical location becomes a real directory of per-skill symlinks, fed by
the checkout plus anything in SKILLS_EXTRA_SOURCES. Harnesses keep their one
directory link, so the count is N + one per harness rather than N x harnesses,
which is what #23 was actually about.

The three requirements #27 named, each with a test:
- collisions are logged with both paths and the checkout wins, never resolved
  in silence;
- removing a skill from a source prunes its link;
- anything in the managed directory that is not our symlink is reported and
  left in place — the installer does not delete content it did not create.

doctor learns the same model: sources are recorded at ~/.agents/skills-sources,
a link into a configured source is healthy, a link into an unknown one is not,
and the old count check becomes a per-skill check because a per-skill layout
can lose one skill without changing any total. The pre-#27 wiring is named as
legacy rather than reported as damage. count_skills needed find -L; without it
symlinked skill directories count as zero.

Verified live on koala: migrated in place to 42 per-skill links, then a second
source added a 43rd alongside them, then a re-run without that source pruned it
back to 42. Only doctor finding throughout was the genuine stale plugin.

Closes #27
Bump-Type: minor

.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "skills",
   "description": "Mathias's engineering skills library, plus the hooks and MCP servers that make it enforceable: TDD, clean code, debugging, specs, discovery, CI, and secret hygiene.",
-  "version": "0.8.4",
+  "version": "0.9.0",
   "author": {
     "name": "Mathias",
     "url": "https://git.d-ma.be/mathias"

README.md

@@ -40,16 +40,42 @@ moves — CI bumps it on every release.
 curl -fsSL https://git.d-ma.be/mathias/skills/raw/branch/main/install.sh | bash
 ```
 
-Idempotent. It clones or fast-forwards the checkout, then creates **three**
+Idempotent. It clones or fast-forwards the checkout, then populates one
-symlinks — one directory link per harness, never one per skill:
+**managed directory** and gives each harness a single link to it:
 
-| Link | Target |
+| Path | Target |
 |---|---|
-| `~/.agents/skills` | `$SKILLS_CHECKOUT_DIR/skills` (Pi reads this path directly) |
+| `~/.agents/skills/` | a real directory, one symlink per skill (Pi reads this path directly) |
+| `~/.agents/skills/<skill>` | `$SKILLS_CHECKOUT_DIR/skills/<skill>`, or another configured source |
 | `~/.config/crush/skills` | `~/.agents/skills` |
 | `~/.config/opencode/skills` | `~/.agents/skills` |
 
-Adding a skill wires it everywhere with no re-run.
+Total links are N + one per harness — not N x harnesses, which is what #23 was
+actually about.
+
+### More than one source of skills
+
+`~/.agents/skills` used to be a single link straight at this checkout. That
+encoded an assumption nobody had stated — that this checkout is the only source
+of skills on the host — and on flamingo the only way to install this library
+was to displace Anthropic's official set, which lived in Crush's directory.
+Real capability loss dressed up as a tidy-up (#27).
+
+Point `SKILLS_EXTRA_SOURCES` at any number of extra directories, colon
+separated, each holding `<skill>/SKILL.md`:
+
+```
+SKILLS_EXTRA_SOURCES=~/.config/crush/skills.anthropic bash install.sh
+```
+
+- The checkout is always first and always wins a name collision — but the
+  collision is **logged**, never resolved in silence. Quietly picking one is
+  how stale content wins.
+- Removing a skill from a source removes its link on the next run.
+- Anything in the managed directory that is not a symlink is reported and left
+  alone. install.sh does not delete content it did not create.
+- The source list is recorded at `~/.agents/skills-sources` so `bin/doctor`
+  can tell a link into a known source from a link into a forgotten one.
 
 ### Where the checkout must live
 
@@ -74,6 +100,7 @@ default to point into `~/dev`.
 | `AGENTS_SKILLS_DIR` | `$HOME/.agents/skills` |
 | `CRUSH_SKILLS_DIR` | `$HOME/.config/crush/skills` |
 | `OPENCODE_SKILLS_DIR` | `$HOME/.config/opencode/skills` |
+| `SKILLS_EXTRA_SOURCES` | unset (colon-separated extra source directories) |
 
 Antigravity and Mistral Vibe targets were removed — unused.
 

SKILLS_INDEX.md

@@ -70,17 +70,21 @@ everything load twice.
 
 ### Crush, Pi, OpenCode — run `install.sh`
 
-These have no plugin system, so they get symlinks — but **one directory link
+These have no plugin system, so they get symlinks — but through one managed
-each**, never one per skill:
+directory, never one link per skill per harness:
 
 ```
-~/.agents/skills           -> $SKILLS_CHECKOUT_DIR/skills   (Pi reads this directly)
+~/.agents/skills/          (real directory; Pi reads it directly)
+~/.agents/skills/tdd       -> $SKILLS_CHECKOUT_DIR/skills/tdd
+~/.agents/skills/xlsx      -> $SKILLS_EXTRA_SOURCES entry
 ~/.config/crush/skills     -> ~/.agents/skills
 ~/.config/opencode/skills  -> ~/.agents/skills
 ```
 
-Adding a skill therefore wires it everywhere with no re-run, and a broken link
+Total links are N + one per harness. `SKILLS_EXTRA_SOURCES` (colon-separated
-is one broken link instead of 42.
+directories) lets a second library — Anthropic's official set, for instance —
+live alongside this one instead of being displaced by it; name collisions are
+logged rather than silently resolved, and the checkout wins (#27).
 
 ```
 curl -fsSL https://git.d-ma.be/mathias/skills/raw/branch/main/install.sh | bash
@@ -94,10 +98,11 @@ absolute link stored there is broken on one side by construction. See #23.
 
 ### Check a host
 
-`task doctor` (or `bin/doctor`) reports dangling links, links resolving into a
+`task doctor` (or `bin/doctor`) reports dangling links, links into a source
-foreign checkout, count mismatches, stray entries, and leftover Claude
+nobody configured, skills in the checkout with no link, stray entries, leftover
-symlinks. It also runs automatically at session start via the plugin, so drift
+Claude symlinks, and a Claude Code plugin sitting on an older generation than
-announces itself instead of waiting to be found.
+the host already has. It also runs automatically at session start via the
+plugin, so drift announces itself instead of waiting to be found.
 
 ## Skill Relationships
 

bin/doctor

@@ -39,12 +39,21 @@ SELF_CHECKOUT=$(CDPATH= cd -- "$SELF_DIR/.." && pwd)
 # copy doctor happens to be running from. When invoked as a plugin hook, $0
 # lives in the plugin cache, which is legitimately a second copy: judging the
 # harness links against it would flag every one of them as "outside".
+AGENTS_DIR="$HOME/.agents/skills"
+SOURCES_FILE="$(dirname -- "$AGENTS_DIR")/$(basename -- "$AGENTS_DIR")-sources"
+
 if [ -n "${DOCTOR_CHECKOUT:-}" ]; then
   CHECKOUT="$DOCTOR_CHECKOUT"
-elif [ -d "$HOME/.agents/skills" ]; then
+elif [ -f "$SOURCES_FILE" ]; then
-  # Resolve the link FIRST, then take the parent. "cd X/.." resolves ".."
+  # Since #27 the canonical location is a real directory fed by several
-  # lexically against the link path, which lands back in ~/.agents.
+  # sources, so it can no longer be resolved to a checkout. install.sh records
-  _resolved=$(CDPATH= cd -- "$HOME/.agents/skills" 2>/dev/null && pwd -P)
+  # the list; the first line is always this repo's skills/ directory.
+  CHECKOUT=$(dirname -- "$(head -n 1 "$SOURCES_FILE")")
+elif [ -L "$AGENTS_DIR" ]; then
+  # Pre-#27 wiring: one link straight at the checkout. Resolve the link FIRST,
+  # then take the parent. "cd X/.." resolves ".." lexically against the link
+  # path, which lands back in ~/.agents.
+  _resolved=$(CDPATH= cd -- "$AGENTS_DIR" 2>/dev/null && pwd -P)
   CHECKOUT=$(dirname -- "$_resolved")
 else
   CHECKOUT="$SELF_CHECKOUT"
@@ -66,9 +75,26 @@ add() {
 }
 
 # count_skills <dir> — directories containing a SKILL.md, one level down.
+# -L on purpose: since #27 the entries are per-skill symlinks, and find does
+# not descend into a symlinked directory without it.
 count_skills() {
   [ -d "$1" ] || { printf '0'; return; }
-  find "$1"/ -mindepth 2 -maxdepth 2 -name SKILL.md 2>/dev/null | wc -l | tr -d ' '
+  find -L "$1"/ -mindepth 2 -maxdepth 2 -name SKILL.md 2>/dev/null | wc -l | tr -d ' '
+}
+
+# under_known_source <physical-path> — 0 when the path lies inside a source
+# install.sh recorded, or inside the active checkout.
+under_known_source() {
+  _path=$1
+  _list="$SKILLS_DIR"
+  [ -f "$SOURCES_FILE" ] && _list="$_list
+$(cat "$SOURCES_FILE")"
+  printf '%s\n' "$_list" | while IFS= read -r _src; do
+    [ -n "$_src" ] || continue
+    _real=$(CDPATH= cd -- "$_src" 2>/dev/null && pwd -P) || continue
+    [ -n "$_real" ] || continue
+    case "$_path" in "$_real"/*|"$_real") printf 'yes'; break ;; esac
+  done | grep -q yes
 }
 
 # --- the checkout itself ----------------------------------------------------
@@ -95,10 +121,47 @@ for entry in "$SKILLS_DIR"/*; do
   fi
 done
 
+# --- the canonical directory --------------------------------------------------
+# Pre-#27 this was a symlink at the checkout. It is a real directory now, one
+# per-skill link per skill, fed by every configured source — that is what lets
+# a second library (Anthropic's official set on flamingo) coexist instead of
+# being displaced.
+if [ -L "$AGENTS_DIR" ]; then
+  add WARN legacy "$AGENTS_DIR is the pre-#27 single-link wiring — re-run install.sh to adopt the multi-source layout"
+elif [ -d "$AGENTS_DIR" ]; then
+  for entry in "$AGENTS_DIR"/*; do
+    [ -e "$entry" ] || [ -L "$entry" ] || continue
+    name=$(basename "$entry")
+
+    if [ ! -L "$entry" ]; then
+      add FAIL unmanaged "$AGENTS_DIR/$name is not a link into any source — nothing manages it and nothing updates it"
+      continue
+    fi
+    if [ ! -e "$entry" ]; then
+      add FAIL dangling "$entry -> $(readlink "$entry") (target does not exist)"
+      continue
+    fi
+
+    resolved=$(CDPATH= cd -- "$entry" 2>/dev/null && pwd -P)
+    if [ -n "$resolved" ] && ! under_known_source "$resolved"; then
+      add FAIL outside "$entry resolves to $resolved, an unknown source — it works, so nothing complains, while serving content nobody updates"
+    fi
+  done
+
+  # A per-skill layout can lose one skill without changing any total, so the
+  # invariant is per skill, not a count.
+  for dir in "$SKILLS_DIR"/*/; do
+    [ -f "$dir/SKILL.md" ] || continue
+    name=$(basename "$dir")
+    [ -L "$AGENTS_DIR/$name" ] \
+      || add FAIL missing "$name is in the checkout but has no link in $AGENTS_DIR — re-run install.sh"
+  done
+fi
+
 # --- harness wiring ---------------------------------------------------------
-# Canonical location first; Pi reads it directly and the others link to it.
+# Crush and OpenCode keep their single directory link at the canonical dir;
+# Pi reads it directly and needs no link of its own.
 for dir in \
-  "$HOME/.agents/skills" \
   "$HOME/.config/crush/skills" \
   "$HOME/.config/opencode/skills"
 do
@@ -110,32 +173,23 @@ do
   fi
 
   # A real directory where a link belongs holds content nothing manages: it
-  # cannot receive new skills and silently shadows the checkout. Distinguished
+  # cannot receive new skills and silently shadows the canonical dir. Since
-  # from the foreign-checkout case below because the fix differs — move it
+  # #27 the fix is not only "move it aside" — it can be added as an extra
-  # aside and re-run install.sh, rather than re-point a link.
+  # source instead, which is how flamingo keeps the official Anthropic set.
   if [ ! -L "$dir" ] && [ -d "$dir" ]; then
-    add FAIL unmanaged "$dir is a real directory, not a link into the checkout — it holds $(count_skills "$dir") unmanaged skill(s); move it aside and re-run install.sh"
+    add FAIL unmanaged "$dir is a real directory, not a link into the canonical dir — it holds $(count_skills "$dir") unmanaged skill(s); add it to SKILLS_EXTRA_SOURCES and re-run install.sh, or move it aside"
     continue
   fi
 
-  # Resolve to a physical path and confirm it lands inside THIS checkout.
-  # A link that resolves to a different checkout is the dangerous case: it
-  # works, so nothing complains, while serving stale content.
   resolved=$(CDPATH= cd -- "$dir" 2>/dev/null && pwd -P)
-  canonical=$(CDPATH= cd -- "$SKILLS_DIR" 2>/dev/null && pwd -P)
+  canonical=$(CDPATH= cd -- "$AGENTS_DIR" 2>/dev/null && pwd -P)
-  if [ -n "$resolved" ] && [ "$resolved" != "$canonical" ]; then
+  if [ -n "$resolved" ] && [ -n "$canonical" ] && [ "$resolved" != "$canonical" ]; then
-    add FAIL outside "$dir resolves to $resolved, outside the active checkout $canonical"
+    add FAIL outside "$dir resolves to $resolved, not the canonical $canonical"
-    continue
-  fi
-
-  got=$(count_skills "$dir")
-  if [ "$got" != "$EXPECTED" ]; then
-    add FAIL count "$dir sees $got skills, checkout has $EXPECTED"
   fi
 done
 
 # --- dangling links anywhere under the harness dirs -------------------------
-for dir in "$HOME/.agents/skills" "$HOME/.config/crush/skills" \
+for dir in "$HOME/.config/crush/skills" \
            "$HOME/.config/opencode/skills" "$HOME/.claude/skills"
 do
   [ -d "$dir" ] || continue
@@ -180,10 +234,63 @@ if [ -f "$INSTALLED" ]; then
     || add WARN plugin "skills@mathias is not installed for Claude Code — /plugin marketplace add https://git.d-ma.be/mathias/skills.git"
 fi
 
+# --- Claude Code: which GENERATION of the plugin is installed ---------------
+# Every check above is about symlink paths, which is the wrong shape for the
+# plugin: it is the only channel Claude Code has, and Claude Code gates updates
+# on plugin.json's version. A host that never picked up a release loads all the
+# skills successfully and is simply a generation behind — silently. Found on
+# koala 2026-08-29: installed 0.6.0, marketplace clone 0.7.0, repo 0.8.5,
+# doctor said "clean" (#30).
+#
+# Offline by construction, like the rest of doctor: "available" means the
+# newest manifest already on this host — the active checkout and any
+# marketplace clone — never a fetch.
+manifest_version() {
+  [ -f "$1" ] || return 1
+  grep -q '"name"[[:space:]]*:[[:space:]]*"skills"' "$1" || return 1
+  sed -n 's/.*"version"[[:space:]]*:[[:space:]]*"\([^"]*\)".*/\1/p' "$1" | head -1
+}
+
+# newer_version a b — echoes whichever sorts higher on major.minor.patch.
+newer_version() {
+  printf '%s\n%s\n' "$1" "$2" | awk -F. '
+    { raw[NR] = $0; for (i = 1; i <= 3; i++) n[NR, i] = ($i == "" ? 0 : $i + 0) }
+    END {
+      for (i = 1; i <= 3; i++) {
+        if (n[1, i] > n[2, i]) { print raw[1]; exit }
+        if (n[1, i] < n[2, i]) { print raw[2]; exit }
+      }
+      print raw[1]
+    }'
+}
+
+installed_v=''
+if [ -f "$INSTALLED" ]; then
+  installed_v=$(sed -n '/"skills@mathias"/,/\]/p' "$INSTALLED" \
+    | sed -n 's/.*"version"[[:space:]]*:[[:space:]]*"\([^"]*\)".*/\1/p' | head -1)
+fi
+
+available_v=''
+for manifest in "$CHECKOUT/.claude-plugin/plugin.json" \
+                "$HOME"/.claude/plugins/marketplaces/*/.claude-plugin/plugin.json
+do
+  v=$(manifest_version "$manifest") || continue
+  [ -n "$v" ] || continue
+  if [ -z "$available_v" ]; then
+    available_v=$v
+  else
+    available_v=$(newer_version "$available_v" "$v")
+  fi
+done
+
+if [ -n "$installed_v" ] && [ -n "$available_v" ] && [ "$installed_v" != "$available_v" ]; then
+  add FAIL plugin-version "Claude Code has skills@mathias $installed_v installed but $available_v is available on this host — /plugin update skills@mathias (a host stale enough to matter is running the old doctor, so the first detection may need this run by hand)"
+fi
+
 # --- output -----------------------------------------------------------------
 if [ "$JSON" -eq 1 ]; then
-  printf '{"checkout":"%s","expected":%s,"findings":[%s]}\n' \
+  printf '{"checkout":"%s","expected":%s,"plugin":{"installed":"%s","available":"%s"},"findings":[%s]}\n' \
-    "$CHECKOUT" "$EXPECTED" "${report%,}"
+    "$CHECKOUT" "$EXPECTED" "$installed_v" "$available_v" "${report%,}"
 elif [ "$findings" -gt 0 ]; then
   printf 'skills doctor — %s finding(s), checkout %s\n\n%s\n' \
     "$findings" "$CHECKOUT" "$report"

install.sh

@@ -20,14 +20,24 @@
 # cannot. This script covers the harnesses with no plugin system: Crush, Pi
 # and OpenCode.
 #
-# Wiring model — one directory link per harness, never one per skill:
+# Wiring model — one managed directory, one link per harness:
 #
-#   ~/.agents/skills            -> $CHECKOUT_DIR/skills   (canonical; Pi reads it directly)
+#   ~/.agents/skills/tdd        -> $CHECKOUT_DIR/skills/tdd   (canonical; Pi reads the dir directly)
+#   ~/.agents/skills/xlsx       -> $OTHER_SOURCE/xlsx
 #   ~/.config/crush/skills      -> ~/.agents/skills
 #   ~/.config/opencode/skills   -> ~/.agents/skills
 #
-# Adding a skill to the repo therefore wires it everywhere with no re-run,
+# ~/.agents/skills was itself a link to this checkout until #27. That encoded
-# and a broken link is one broken link rather than 42.
+# an assumption nobody had stated — that this checkout is the ONLY source of
+# skills on the host — and on flamingo the only way to install this library
+# was to displace Anthropic's official set, which lived in Crush's directory.
+# A real directory of per-skill links serves several sources at once: total
+# links are N + one per harness, still not N x harnesses (#23's actual point).
+#
+# Extra sources come from SKILLS_EXTRA_SOURCES, a colon-separated list of
+# directories each holding <skill>/SKILL.md. The checkout is always first and
+# always wins a name collision — but the collision is logged, never resolved
+# in silence, because quietly picking one is how stale content wins.
 #
 # CHECKOUT_DIR deliberately defaults OUTSIDE any file-synced or
 # cross-platform-shared directory. Do not "fix" it to point into ~/dev: on a
@@ -43,6 +53,10 @@ CHECKOUT_DIR="${SKILLS_CHECKOUT_DIR:-$HOME/.local/share/skills}"
 AGENTS_DIR="${AGENTS_SKILLS_DIR:-$HOME/.agents/skills}"
 CRUSH_DIR="${CRUSH_SKILLS_DIR:-$HOME/.config/crush/skills}"
 OPENCODE_DIR="${OPENCODE_SKILLS_DIR:-$HOME/.config/opencode/skills}"
+EXTRA_SOURCES="${SKILLS_EXTRA_SOURCES:-}"
+# Recorded beside the managed directory rather than inside it: a stray file in
+# there would look like a skill to every harness reading the dir.
+SOURCES_MANIFEST="$(dirname "$AGENTS_DIR")/$(basename "$AGENTS_DIR")-sources"
 
 log() { printf '[skills] %s\n' "$*"; }
 
@@ -74,6 +88,95 @@ count_skills() {
   find "$CHECKOUT_DIR/skills" -mindepth 2 -maxdepth 2 -name SKILL.md 2>/dev/null | wc -l | tr -d ' '
 }
 
+# sources — every configured source directory, primary first, one per line.
+sources() {
+  printf '%s\n' "$CHECKOUT_DIR/skills"
+  [ -n "$EXTRA_SOURCES" ] || return 0
+  # printf '%s\n' deliberately: without the trailing newline `read` hits EOF
+  # on the final entry and the loop body never runs for it.
+  printf '%s\n' "$EXTRA_SOURCES" | tr ':' '\n' | while IFS= read -r src; do
+    [ -n "$src" ] || continue
+    if [ -d "$src" ]; then
+      printf '%s\n' "$src"
+    else
+      log "extra source $src does not exist — skipping"
+    fi
+  done
+}
+
+# prepare_agents_dir — the canonical location is a real directory now. A host
+# still on the single-link wiring is migrated in place.
+prepare_agents_dir() {
+  if [ -L "$AGENTS_DIR" ]; then
+    log "migrating $AGENTS_DIR from the single-link wiring to a per-skill directory"
+    rm -f "$AGENTS_DIR"
+  elif [ -e "$AGENTS_DIR" ] && [ ! -d "$AGENTS_DIR" ]; then
+    log "REFUSING to replace $AGENTS_DIR — it exists and is not a directory"
+    return 1
+  fi
+  mkdir -p "$AGENTS_DIR"
+}
+
+# wire_skills — one symlink per skill, from every configured source.
+wire_skills() {
+  local src_list desired name src dir link target
+  src_list="$(mktemp)"
+  sources > "$src_list"
+
+  desired=""
+  while IFS= read -r src; do
+    [ -d "$src" ] || continue
+    for dir in "$src"/*/; do
+      [ -f "$dir/SKILL.md" ] || continue
+      name="$(basename "$dir")"
+      target="${dir%/}"
+
+      if printf '%s' "$desired" | grep -qx -- "$name"; then
+        log "COLLISION: $name is offered by $target too; keeping $AGENTS_DIR/$name -> $(readlink "$AGENTS_DIR/$name" 2>/dev/null || echo '?')"
+        continue
+      fi
+
+      link="$AGENTS_DIR/$name"
+      if [ -L "$link" ]; then
+        if [ "$(readlink "$link")" = "$target" ]; then
+          desired="$desired$name
+"
+          continue
+        fi
+        rm -f "$link"
+      elif [ -e "$link" ]; then
+        log "unmanaged: $link is not a symlink — left in place; move it aside to let $target take the name"
+        continue
+      fi
+      ln -s "$target" "$link"
+      desired="$desired$name
+"
+    done
+  done < "$src_list"
+  rm -f "$src_list"
+
+  # Removing a skill from a source must remove its link, or the previous
+  # generation's problem (links resolving to nothing, invisible to git)
+  # returns in a new shape.
+  for link in "$AGENTS_DIR"/*; do
+    [ -e "$link" ] || [ -L "$link" ] || continue
+    name="$(basename "$link")"
+    if [ ! -L "$link" ]; then
+      log "unmanaged: $link is not a symlink and no source offers it — left in place"
+      continue
+    fi
+    printf '%s' "$desired" | grep -qx -- "$name" && continue
+    rm -f "$link"
+    log "pruned $name — no configured source offers it any more"
+  done
+
+  sources > "$SOURCES_MANIFEST"
+  # Reported through a global, not stdout: wire_skills logs collisions and
+  # unmanaged entries as it goes, and capturing its stdout for a count would
+  # swallow exactly the warnings this change exists to surface.
+  LINKED_COUNT=$(printf '%s' "$desired" | grep -c . || true)
+}
+
 # link_dir <link_path> <target_path>
 # Replaces whatever is there — including a directory left behind by the old
 # per-skill wiring — with a single symlink.
@@ -104,12 +207,14 @@ main() {
 
   # Canonical location. Pi reads ~/.agents/skills directly, so it needs no
   # harness-specific link of its own.
-  link_dir "$AGENTS_DIR" "$CHECKOUT_DIR/skills"
+  prepare_agents_dir
+  LINKED_COUNT=0
+  wire_skills
 
   link_dir "$CRUSH_DIR" "$AGENTS_DIR"
   link_dir "$OPENCODE_DIR" "$AGENTS_DIR"
 
-  log "done — $(count_skills) skill(s) at ref=$REF, 3 links total"
+  log "done — $LINKED_COUNT skill(s) linked from $(sources | wc -l | tr -d ' ') source(s), ref=$REF"
   log "Claude Code: install the plugin instead — /plugin marketplace add $REPO_URL"
 }
 

tests/doctor_test.sh

@@ -37,11 +37,21 @@ new_fixture() {
   printf '%s' "$_f"
 }
 
-# wire_clean <fixture> — the correct wiring: one canonical link, harnesses
+# wire_clean <fixture> [extra-source-dir] — the correct wiring since #27: the
-# pointing at it.
+# canonical location is a REAL directory of per-skill links, fed by one or more
+# sources, with each harness keeping its single directory link to it.
 wire_clean() {
-  mkdir -p "$1/home/.agents" "$1/home/.config/crush" "$1/home/.config/opencode"
+  mkdir -p "$1/home/.agents/skills" "$1/home/.config/crush" "$1/home/.config/opencode"
-  ln -sfn "$1/ck/skills" "$1/home/.agents/skills"
+  for _d in "$1"/ck/skills/*/; do
+    ln -sfn "${_d%/}" "$1/home/.agents/skills/$(basename "$_d")"
+  done
+  printf '%s\n' "$1/ck/skills" > "$1/home/.agents/skills-sources"
+  if [ -n "${2:-}" ]; then
+    for _d in "$2"/*/; do
+      ln -sfn "${_d%/}" "$1/home/.agents/skills/$(basename "$_d")"
+    done
+    printf '%s\n' "$2" >> "$1/home/.agents/skills-sources"
+  fi
   ln -sfn "$1/home/.agents/skills" "$1/home/.config/crush/skills"
   ln -sfn "$1/home/.agents/skills" "$1/home/.config/opencode/skills"
 }
@@ -79,27 +89,43 @@ assert_clean "$f" 'clean fixture exits 0'
 
 # --- 2. dangling link (the 243-link case, gitignored and invisible) ----------
 f=$(new_fixture dangling); wire_clean "$f"
-ln -sfn "$f/ck/skills-that-moved" "$f/home/.agents/skills"
+ln -sfn "$f/ck/skills/vanished" "$f/home/.agents/skills/alpha"
-assert_fails "$f" 'dangling' 'dangling canonical link is reported'
+assert_fails "$f" 'dangling' 'dangling per-skill link is reported'
 
-# --- 3. resolves, but to a DIFFERENT checkout (the silent-stale case) --------
+# --- 3. resolves, but into a source nobody configured (silent-stale case) ----
 # Worse than dangling: it works, so nothing complains, while serving content
-# from a checkout that is months behind.
+# from a checkout that is months behind. Since #27 a link may legitimately
+# point outside the checkout — but only into a source the installer recorded.
 f=$(new_fixture stale)
-mkdir -p "$f/other/skills/alpha" "$f/other/skills/beta"
+mkdir -p "$f/other/alpha"
-printf -- '---\nname: alpha\ndescription: a\n---\n' > "$f/other/skills/alpha/SKILL.md"
+printf -- '---\nname: alpha\ndescription: a\n---\n' > "$f/other/alpha/SKILL.md"
-printf -- '---\nname: beta\ndescription: b\n---\n' > "$f/other/skills/beta/SKILL.md"
 wire_clean "$f"
-ln -sfn "$f/other/skills" "$f/home/.agents/skills"
+ln -sfn "$f/other/alpha" "$f/home/.agents/skills/alpha"
-assert_fails "$f" 'outside' 'link into a foreign checkout is reported'
+assert_fails "$f" 'unknown source' 'link into an unconfigured source is reported'
 
-# --- 4. count mismatch (a harness seeing fewer skills than the checkout) -----
+# --- 3b. a link into a CONFIGURED extra source is healthy -------------------
-f=$(new_fixture count)
+# The whole point of #27: Anthropic's official set alongside this library.
-mkdir -p "$f/home/.config/crush/skills/alpha"
+f=$(new_fixture multisource)
-printf -- '---\nname: alpha\ndescription: a\n---\n' > "$f/home/.config/crush/skills/alpha/SKILL.md"
+mkdir -p "$f/other/xlsx"
-mkdir -p "$f/home/.agents"
+printf -- '---\nname: xlsx\ndescription: x\n---\n' > "$f/other/xlsx/SKILL.md"
+wire_clean "$f" "$f/other"
+assert_clean "$f" 'a link into a configured extra source is healthy'
+
+# --- 3c. the pre-#27 single-link wiring is named, not mistaken for damage ----
+f=$(new_fixture legacy)
+mkdir -p "$f/home/.agents" "$f/home/.config/crush" "$f/home/.config/opencode"
 ln -sfn "$f/ck/skills" "$f/home/.agents/skills"
-assert_fails "$f" 'count' 'skill-count mismatch is reported'
+ln -sfn "$f/home/.agents/skills" "$f/home/.config/crush/skills"
+ln -sfn "$f/home/.agents/skills" "$f/home/.config/opencode/skills"
+assert_fails "$f" 'single-link' 'legacy single-link wiring is reported as such'
+
+# --- 4. a skill in the checkout with no link anywhere ------------------------
+# The multi-source replacement for the old count check: with per-skill links a
+# skill can be missing individually, which a total count would hide if an extra
+# source happened to supply the same number.
+f=$(new_fixture missing); wire_clean "$f"
+rm -f "$f/home/.agents/skills/beta"
+assert_fails "$f" 'beta' 'a checkout skill with no link is reported'
 
 # --- 5. stray entry (the loose secret-hygiene.md that loaded nowhere) --------
 f=$(new_fixture stray); wire_clean "$f"
@@ -119,9 +145,9 @@ assert_fails "$f" 'legacy' 'leftover per-skill Claude symlinks are reported'
 # resolution target, which is true but useless. It must say the dir is not a
 # link at all, because the fix (move it aside, re-run install.sh) is different
 # from the fix for a link into a foreign checkout.
-f=$(new_fixture realdir)
+f=$(new_fixture realdir); wire_clean "$f"
-mkdir -p "$f/home/.agents" "$f/home/.config/crush/skills/alpha"
+rm -f "$f/home/.config/crush/skills"
-ln -sfn "$f/ck/skills" "$f/home/.agents/skills"
+mkdir -p "$f/home/.config/crush/skills/alpha"
 printf -- '---\nname: alpha\ndescription: a\n---\n' > "$f/home/.config/crush/skills/alpha/SKILL.md"
 assert_fails "$f" 'not a link' 'real directory is reported as unmanaged, not as "outside"'
 
@@ -133,5 +159,63 @@ mkdir -p "$f/home/.claude/skills"
 ln -sfn "$f/ck/skills/vanished" "$f/home/.claude/skills/vanished"
 assert_fails "$f" 'dangling' 'dangling link inside a harness dir is reported'
 
+# --- 8. Claude Code plugin pinned to an older version than is available -----
+# The plugin is the ONLY delivery channel for Claude Code, and Claude Code
+# gates updates on plugin.json's version field. A host that never picked the
+# new one up loads every skill successfully — just the wrong generation. Found
+# live on koala 2026-08-29: installed 0.6.0, marketplace 0.7.0, repo 0.8.5,
+# and doctor said "clean" (#30).
+
+# installed_state <fixture> <version> — the Claude Code install record.
+installed_state() {
+  mkdir -p "$1/home/.claude/plugins"
+  cat > "$1/home/.claude/plugins/installed_plugins.json" <<JSON
+{
+  "version": 2,
+  "plugins": {
+    "skills@mathias": [
+      {
+        "scope": "user",
+        "installPath": "/somewhere/$2",
+        "version": "$2"
+      }
+    ]
+  }
+}
+JSON
+}
+
+# manifest <dir> <version> — a .claude-plugin/plugin.json under <dir>.
+manifest() {
+  mkdir -p "$1/.claude-plugin"
+  printf '{\n  "name": "skills",\n  "version": "%s"\n}\n' "$2" > "$1/.claude-plugin/plugin.json"
+}
+
+f=$(new_fixture pluginmatch); wire_clean "$f"
+installed_state "$f" 0.8.0
+manifest "$f/ck" 0.8.0
+assert_clean "$f" 'plugin on the current version stays silent'
+
+f=$(new_fixture pluginstale); wire_clean "$f"
+installed_state "$f" 0.7.0
+manifest "$f/ck" 0.8.0
+assert_fails "$f" '0.7.0' 'stale plugin version is reported'
+assert_fails "$f" '0.8.0' 'stale plugin report names the available version'
+
+# A host that only uses the symlink path has no install record at all. That is
+# a valid configuration and must not fail.
+f=$(new_fixture pluginabsent); wire_clean "$f"
+manifest "$f/ck" 0.8.0
+assert_clean "$f" 'no Claude Code install record is not a fault'
+
+# The marketplace clone is what Claude Code compares against, so a newer
+# version there means an update is waiting even when the local checkout agrees
+# with what is installed.
+f=$(new_fixture pluginmarket); wire_clean "$f"
+installed_state "$f" 0.7.0
+manifest "$f/ck" 0.7.0
+manifest "$f/home/.claude/plugins/marketplaces/mathias" 0.9.0
+assert_fails "$f" '0.9.0' 'a newer marketplace clone is reported'
+
 printf '\ndoctor: %d passed, %d failed\n' "$pass" "$fail"
 [ "$fail" -eq 0 ]

tests/install_test.sh

@@ -0,0 +1,160 @@
+#!/bin/sh
+# Tests for install.sh's wiring model.
+#
+# The regression these exist for: install.sh wired each harness with ONE
+# directory symlink to this checkout, which quietly encoded "this checkout is
+# the only source of skills on the host". On flamingo the Crush directory held
+# Anthropic's official skill set, and the only way to install this library was
+# to displace it — a real capability loss dressed up as a tidy-up (#27).
+#
+# Fixtures drive install.sh entirely through env seams, so no test touches the
+# real host wiring.
+
+set -u
+
+ROOT=$(CDPATH= cd -- "$(dirname -- "$0")/.." && pwd)
+SUT="$ROOT/install.sh"
+
+pass=0
+fail=0
+WORK=${TMPDIR:-/tmp}/install_test.$$
+
+if [ ! -f "$SUT" ]; then
+  printf 'FAIL: %s does not exist\n' "$SUT"
+  exit 1
+fi
+
+cleanup() { rm -rf "$WORK"; }
+trap cleanup EXIT INT TERM
+
+ok() { pass=$((pass + 1)); printf '  ok   %s\n' "$1"; }
+no() { fail=$((fail + 1)); printf '  FAIL %s\n%s\n' "$1" "${2:-}"; }
+
+# skill <dir> <name> — a minimal valid skill.
+skill() {
+  mkdir -p "$1/$2"
+  printf -- '---\nname: %s\ndescription: d\n---\n' "$2" > "$1/$2/SKILL.md"
+}
+
+# new_fixture <name> [extra-source-names...] — checkout with alpha+beta.
+new_fixture() {
+  _f="$WORK/$1"
+  mkdir -p "$_f/ck/skills" "$_f/home"
+  skill "$_f/ck/skills" alpha
+  skill "$_f/ck/skills" beta
+  printf '%s' "$_f"
+}
+
+# run_install <fixture> [extra-sources] — echoes output, sets $rc.
+run_install() {
+  _f=$1
+  _extra=${2:-}
+  _out=$(HOME="$_f/home" \
+    SKILLS_SKIP_FETCH=1 \
+    SKILLS_CHECKOUT_DIR="$_f/ck" \
+    AGENTS_SKILLS_DIR="$_f/home/.agents/skills" \
+    CRUSH_SKILLS_DIR="$_f/home/.config/crush/skills" \
+    OPENCODE_SKILLS_DIR="$_f/home/.config/opencode/skills" \
+    SKILLS_EXTRA_SOURCES="$_extra" \
+    bash "$SUT" 2>&1)
+  rc=$?
+  printf '%s' "$_out"
+}
+
+# --- 1. the new shape: a real directory of per-skill links -------------------
+f=$(new_fixture fresh)
+out=$(run_install "$f")
+A="$f/home/.agents/skills"
+if [ ! -d "$A" ] || [ -L "$A" ]; then
+  no 'agents dir is a real directory' "$out"
+elif [ ! -L "$A/alpha" ] || [ ! -L "$A/beta" ]; then
+  no 'each skill is its own link' "$out"
+elif [ ! -L "$f/home/.config/crush/skills" ] || [ ! -L "$f/home/.config/opencode/skills" ]; then
+  no 'harnesses keep one directory link each' "$out"
+else
+  ok 'fresh install builds per-skill links under a real agents dir'
+fi
+
+# --- 2. a second source is served WITHOUT displacing the first --------------
+f=$(new_fixture twosource)
+mkdir -p "$f/other"
+skill "$f/other" xlsx
+out=$(run_install "$f" "$f/other")
+if [ -L "$f/home/.agents/skills/xlsx" ] && [ -L "$f/home/.agents/skills/alpha" ]; then
+  ok 'a second source is linked alongside the checkout'
+else
+  no 'a second source is linked alongside the checkout' "$out"
+fi
+
+# --- 3. name collisions are REPORTED, never silently resolved ---------------
+# Two sources offering `code-review` is a real possibility, and picking one
+# quietly is how stale content wins.
+f=$(new_fixture collide)
+mkdir -p "$f/other"
+skill "$f/other" alpha
+out=$(run_install "$f" "$f/other")
+if printf '%s' "$out" | grep -qi 'collision' \
+   && printf '%s' "$out" | grep -q "$f/other/alpha"; then
+  target=$(readlink "$f/home/.agents/skills/alpha")
+  if [ "$target" = "$f/ck/skills/alpha" ]; then
+    ok 'a name collision is reported and the checkout wins'
+  else
+    no 'a name collision is reported and the checkout wins' "resolved to $target"
+  fi
+else
+  no 'a name collision is reported and the checkout wins' "$out"
+fi
+
+# --- 4. removing a skill from a source removes its link ---------------------
+# Without this the previous generation's problem returns in a new shape: links
+# that resolve to nothing, invisible to git.
+f=$(new_fixture prune)
+out=$(run_install "$f")
+rm -rf "$f/ck/skills/beta"
+out=$(run_install "$f")
+if [ -e "$f/home/.agents/skills/beta" ] || [ -L "$f/home/.agents/skills/beta" ]; then
+  no 'a removed skill loses its link' "$out"
+else
+  ok 'a removed skill loses its link'
+fi
+
+# --- 5. migration from the old single-link shape ----------------------------
+f=$(new_fixture migrate)
+mkdir -p "$f/home/.agents"
+ln -s "$f/ck/skills" "$f/home/.agents/skills"
+out=$(run_install "$f")
+if [ -L "$f/home/.agents/skills" ]; then
+  no 'the old single-link wiring is migrated in place' "$out"
+elif [ -L "$f/home/.agents/skills/alpha" ]; then
+  ok 'the old single-link wiring is migrated in place'
+else
+  no 'the old single-link wiring is migrated in place' "$out"
+fi
+
+# --- 6. unmanaged real content in the agents dir is never deleted -----------
+f=$(new_fixture protect)
+mkdir -p "$f/home/.agents/skills"
+skill "$f/home/.agents/skills" handwritten
+out=$(run_install "$f")
+if [ -f "$f/home/.agents/skills/handwritten/SKILL.md" ] \
+   && printf '%s' "$out" | grep -qi 'unmanaged'; then
+  ok 'unmanaged content is reported and left in place'
+else
+  no 'unmanaged content is reported and left in place' "$out"
+fi
+
+# --- 7. the source list is recorded for doctor ------------------------------
+f=$(new_fixture manifest)
+mkdir -p "$f/other"
+skill "$f/other" xlsx
+out=$(run_install "$f" "$f/other")
+if [ -f "$f/home/.agents/skills-sources" ] \
+   && grep -q "$f/other" "$f/home/.agents/skills-sources" \
+   && grep -q "$f/ck/skills" "$f/home/.agents/skills-sources"; then
+  ok 'configured sources are recorded for doctor'
+else
+  no 'configured sources are recorded for doctor' "$out"
+fi
+
+printf '\ninstall: %d passed, %d failed\n' "$pass" "$fail"
+[ "$fail" -eq 0 ]