Fix skills: replace \${} with \$VAR to pass Bash permission checks

Claude Code's Bash permission checker rejects \${VAR} parameter
substitution in skill ! commands. Replace all occurrences with \$VAR
(identical shell expansion) across log, reflect-logs, and
distill-best-practices skills. Rewrite \${VAR:-default} to use
test -n / || pattern instead.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

skills/distill-best-practices/SKILL.md

@@ -14,35 +14,55 @@ You are extracting generalisable best practices from project-specific memory fil
 
 ## Pre-gathered context
 
+### CLAUDE_PROJECT_ROOT
+!`test -n "$CLAUDE_PROJECT_ROOT" && echo "$CLAUDE_PROJECT_ROOT" || echo "NOT_SET"`
+
 ### Distill state
-!`cat ../claude-foundations/best-practices/.distill-state.json 2>/dev/null || echo "{}"`
+!`cat $CLAUDE_PROJECT_ROOT/projects/claude-foundations/best-practices/.distill-state.json 2>/dev/null || echo "{}"`
 
 ### Settings
-!`cat settings.yaml 2>/dev/null || cat ../claude-foundations/settings.yaml 2>/dev/null || echo "No settings file found"`
+!`cat $CLAUDE_PROJECT_ROOT/projects/claude-foundations/settings.yaml 2>/dev/null || echo "Settings not found — CLAUDE_PROJECT_ROOT may not be set"`
 
 ### Current best-practices index
-!`cat ../claude-foundations/BESTPRACTICES.md 2>/dev/null || echo "No index found"`
+!`cat $CLAUDE_PROJECT_ROOT/projects/claude-foundations/BESTPRACTICES.md 2>/dev/null || echo "Index not found"`
 
 ### Available best-practices files
-!`ls -1 ../claude-foundations/best-practices/ 2>/dev/null || echo "No best-practices directory"`
+!`ls -1 $CLAUDE_PROJECT_ROOT/projects/claude-foundations/best-practices/ 2>/dev/null || echo "No best-practices directory"`
 
 ### Projects directory listing
-!`ls -1d ../*/ 2>/dev/null || echo "No projects directory"`
+!`ls -1d $CLAUDE_PROJECT_ROOT/projects/*/ 2>/dev/null || echo "No projects directory"`
 
 ## Instructions
 
+### Step 0: Detect project root
+
+Check the pre-gathered `CLAUDE_PROJECT_ROOT` value above. If it shows `NOT_SET` or the pre-gathered context is missing:
+
+1. Walk up from the current working directory to find the **highest** parent directory containing a `CLAUDE.md` file — that is the project root.
+2. Use that path as `PROJECT_ROOT` for all subsequent steps.
+
+If `CLAUDE_PROJECT_ROOT` was set, use that value as `PROJECT_ROOT`.
+
+The key paths derived from the root:
+- **Settings**: `<PROJECT_ROOT>/projects/claude-foundations/settings.yaml`
+- **Best practices dir**: `<PROJECT_ROOT>/projects/claude-foundations/best-practices/`
+- **Best practices index**: `<PROJECT_ROOT>/projects/claude-foundations/BESTPRACTICES.md`
+- **Distill state**: `<PROJECT_ROOT>/projects/claude-foundations/best-practices/.distill-state.json`
+
 ### Step 1: Discover changes per project
 
-Read `settings.yaml` for the list of tracked projects and `projects_dir`.
+Read `settings.yaml` (pre-gathered above, or read it now if Step 0 detected the root manually).
 
-For each project in `distill.projects`:
+For each project in `distill.projects`, get its path: `<PROJECT_ROOT>/<projects_dir>/<project_name>`.
+Also process any `distill.extra_projects` entries — these have a `path` field relative to `PROJECT_ROOT`.
 
-1. Get the project path: `<projects_dir>/<project_name>`
-2. Get current HEAD: `git -C <path> rev-parse HEAD`
-3. Look up `last_sha` from `.distill-state.json` for this project
-4. If SHA matches → skip this project (no changes)
-5. If `last_sha` exists → find changed files: `git -C <path> diff --name-only <last_sha>..HEAD -- memory/`
-6. If `last_sha` is missing (first run) → list all memory files: `ls <path>/memory/*.md`
+For each project (from both lists):
+
+1. Get current HEAD: `git -C <path> rev-parse HEAD`
+2. Look up `last_sha` from `.distill-state.json` for this project
+3. If SHA matches → skip this project (no changes)
+4. If `last_sha` exists → find changed files: `git -C <path> diff --name-only <last_sha>..HEAD -- memory/`
+5. If `last_sha` is missing (first run) → list all memory files: `ls <path>/memory/*.md`
 
 Filter to only `memory/*.md` files (exclude `memory/log/` — those are raw, unprocessed).
 
@@ -106,11 +126,11 @@ For each approved proposal:
 
 If a new best-practices topic file is needed:
 - Create it following the format of existing files (top-level heading, subheadings per entry, 2-6 lines per entry)
-- Add it to `BESTPRACTICES.md` (in the claude-foundations project root) with a one-line description
+- Add it to `<PROJECT_ROOT>/projects/claude-foundations/BESTPRACTICES.md` with a one-line description
 
 ### Step 6: Update distill state
 
-Write `best-practices/.distill-state.json`:
+Write `<PROJECT_ROOT>/projects/claude-foundations/best-practices/.distill-state.json`:
 
 ```json
 {

skills/log/SKILL.md

@@ -21,7 +21,7 @@ You are capturing key points from the current session into a structured log file
 !`ls -1 memory/log/ 2>/dev/null || echo "No log directory yet"`
 
 ### Settings
-!`cat settings.yaml 2>/dev/null || cat ../claude-foundations/settings.yaml 2>/dev/null || echo "No settings file found — using defaults: retention_days=7, warn_unreflected_days=14"`
+!`cat settings.yaml 2>/dev/null || cat $CLAUDE_PROJECT_ROOT/projects/claude-foundations/settings.yaml 2>/dev/null || echo "No settings file found — using defaults: retention_days=7, warn_unreflected_days=14"`
 
 ### Reflection state (to check what has been reflected)
 !`cat .reflection-state.json 2>/dev/null || echo "No reflection state yet"`

skills/reflect-logs/SKILL.md

@@ -26,7 +26,7 @@ You are processing session logs into structured, topic-based memory files.
 !`ls -1 memory/ 2>/dev/null || echo "No memory directory"`
 
 ### Settings
-!`cat settings.yaml 2>/dev/null || cat ../claude-foundations/settings.yaml 2>/dev/null || echo "No settings file found — using defaults: max_logs_per_run=10, retention_days=7, warn_unreflected_days=14"`
+!`cat settings.yaml 2>/dev/null || cat $CLAUDE_PROJECT_ROOT/projects/claude-foundations/settings.yaml 2>/dev/null || echo "No settings file found — using defaults: max_logs_per_run=10, retention_days=7, warn_unreflected_days=14"`
 
 ### Recent git log (for staleness detection)
 !`git log --oneline -30 2>/dev/null || echo "Not a git repo"`