fix: disable_plugin_hooks toggle, setup template references, Linux stat

- Add disable_plugin_hooks config key to vaultguard.sh (closes agenticnotetaking#23)
- Fix setup skill to read hook templates instead of improvising (fixes
  double-execution when both plugin and project hooks exist)
- Fix stat -f ambiguity on Linux in session-orient.sh (closes agenticnotetaking#16)

Author: matt-kommon

hooks/scripts/session-orient.sh

@@ -139,10 +139,10 @@ fi
 
 # Methodology staleness check (Rule Zero)
 if [ -d ops/methodology ] && [ -f ops/config.yaml ]; then
-  CONFIG_MTIME=$(stat -f %m ops/config.yaml 2>/dev/null || stat -c %Y ops/config.yaml 2>/dev/null || echo 0)
+  CONFIG_MTIME=$(stat -c %Y ops/config.yaml 2>/dev/null || stat -f %m ops/config.yaml 2>/dev/null || echo 0)
   NEWEST_METH=$(ls -t ops/methodology/*.md 2>/dev/null | head -1)
   if [ -n "$NEWEST_METH" ]; then
-    METH_MTIME=$(stat -f %m "$NEWEST_METH" 2>/dev/null || stat -c %Y "$NEWEST_METH" 2>/dev/null || echo 0)
+    METH_MTIME=$(stat -c %Y "$NEWEST_METH" 2>/dev/null || stat -f %m "$NEWEST_METH" 2>/dev/null || echo 0)
     DAYS_STALE=$(( (CONFIG_MTIME - METH_MTIME) / 86400 ))
     if [ "$DAYS_STALE" -ge 30 ]; then
       echo "CONDITION: Methodology notes are ${DAYS_STALE}+ days behind config changes. Consider /rethink drift."

hooks/scripts/vaultguard.sh

@@ -21,6 +21,10 @@ git: true
 session_capture: true
 EOF
   fi
+  # Check if plugin hooks are disabled (project hooks take over)
+  if grep -q '^disable_plugin_hooks: true' "$MARKER" 2>/dev/null; then
+    exit 1
+  fi
   exit 0
 fi
 

skills/setup/SKILL.md

@@ -1416,7 +1416,24 @@ For Claude Code, add to `.claude/settings.json` (using additive merge).
 
 **Critical:** The old flat format (`"type": "command"` at the matcher level) is rejected by Claude Code. Each event must use the nested structure: `"EventName": [{ "matcher": "...", "hooks": [{ "type": "command", "command": "..." }] }]`.
 
-Generate all four hook scripts: session-orient.sh, session-capture.sh, validate-note.sh, auto-commit.sh.
+Generate all four hook scripts by reading and vocabulary-transforming the templates:
+
+1. Read `${CLAUDE_PLUGIN_ROOT}/platforms/claude-code/hooks/session-orient.sh.template`
+2. Read `${CLAUDE_PLUGIN_ROOT}/platforms/claude-code/hooks/session-capture.sh.template`
+3. Read `${CLAUDE_PLUGIN_ROOT}/platforms/claude-code/hooks/write-validate.sh.template`
+4. Read `${CLAUDE_PLUGIN_ROOT}/platforms/claude-code/hooks/auto-commit.sh.template`
+
+For each template:
+- Replace `{{NOTES_DIR:-notes}}` with the vocabulary-mapped notes directory
+- Replace `{{INBOX_DIR:-inbox}}` with the vocabulary-mapped inbox directory
+- Replace `{{OBS_THRESHOLD:-10}}` with the configured observation threshold (default 10)
+- Replace `{{TENSION_THRESHOLD:-5}}` with the configured tension threshold (default 5)
+- Replace `/{DOMAIN:rethink}`, `/{DOMAIN:reduce}`, `/{DOMAIN:reflect}` with vocabulary-mapped skill names
+- Replace `{{DOMAIN:note}}`, `{{DOMAIN:topic_map}}` with vocabulary-mapped terms
+- Remove `{{IF_SELF_SPACE}}` / `{{END_IF_SELF_SPACE}}` comment markers (keep content if self-space is active, remove block if not)
+- Remove `{{IF_DISCOVERY_NUDGE}}` / `{{END_IF_DISCOVERY_NUDGE}}` comment markers (keep content if discovery nudge is active, remove block if not)
+
+Write the transformed scripts to `.claude/hooks/`. CRITICAL: Do NOT generate hook scripts from scratch or improvise their content. The templates contain session tracking, context injection, and condition checks that must be preserved.
 
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