Generate skills into temp dir to avoid polluting git status

- generate-skills.py now respects SKILLS_DIR env var
- launchme.sh and updateme.sh generate into mktemp -d, copy to vault,
  then clean up — no more untracked skills/ left in the repo
- Warn the user when python3 is missing so Cowork/Desktop users know
  why .claude/skills/ is absent

scripts/generate-skills.py

@@ -16,7 +16,7 @@ import os, re, sys
 
 ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 AGENTS_DIR = os.path.join(ROOT, "agents")
-SKILLS_DIR = os.path.join(ROOT, "skills")
+SKILLS_DIR = os.environ.get("SKILLS_DIR", os.path.join(ROOT, "skills"))
 
 
 def parse_agent(path: str):

scripts/launchme.sh

@@ -82,12 +82,12 @@ success "Copied references"
 SKILL_COUNT=0
 if command -v python3 >/dev/null 2>&1 && [[ -f "$REPO_DIR/scripts/generate-skills.py" ]]; then
   info "Generating skills from agents..."
-  python3 "$REPO_DIR/scripts/generate-skills.py" >/dev/null 2>&1
-fi
+  SKILLS_TMP="$(mktemp -d)"
+  SKILLS_DIR="$SKILLS_TMP" python3 "$REPO_DIR/scripts/generate-skills.py" >/dev/null 2>&1 || true
 
-if [[ -d "$REPO_DIR/skills" ]]; then
+  if [[ -d "$SKILLS_TMP" ]] && ls "$SKILLS_TMP"/*/SKILL.md >/dev/null 2>&1; then
     info "Creating .claude/skills/ in vault..."
-  for skill_dir in "$REPO_DIR/skills/"*/; do
+    for skill_dir in "$SKILLS_TMP/"*/; do
       skill_name="$(basename "$skill_dir")"
       mkdir -p "$VAULT_DIR/.claude/skills/$skill_name"
       cp "$skill_dir"* "$VAULT_DIR/.claude/skills/$skill_name/" 2>/dev/null || true
@@ -96,6 +96,12 @@ if [[ -d "$REPO_DIR/skills" ]]; then
     success "Copied $SKILL_COUNT skills"
   fi
 
+  rm -rf "$SKILLS_TMP"
+else
+  warn "python3 not found — skipped skills generation (Cowork/Desktop won't have skills)"
+  warn "Install Python 3 and re-run this script to enable Cowork/Desktop support"
+fi
+
 # ── Copy CLAUDE.md ───────────────────────────────────────────────────────────
 if [[ -f "$REPO_DIR/CLAUDE.md" ]]; then
   cp "$REPO_DIR/CLAUDE.md" "$VAULT_DIR/CLAUDE.md"

scripts/updateme.sh

@@ -77,11 +77,11 @@ done
 # ── Regenerate and update skills ───────────────────────────────────────────
 SKILL_COUNT=0
 if command -v python3 >/dev/null 2>&1 && [[ -f "$REPO_DIR/scripts/generate-skills.py" ]]; then
-  python3 "$REPO_DIR/scripts/generate-skills.py" >/dev/null 2>&1
-fi
+  SKILLS_TMP="$(mktemp -d)"
+  SKILLS_DIR="$SKILLS_TMP" python3 "$REPO_DIR/scripts/generate-skills.py" >/dev/null 2>&1 || true
 
-if [[ -d "$REPO_DIR/skills" ]]; then
-  for skill_dir in "$REPO_DIR/skills/"*/; do
+  if [[ -d "$SKILLS_TMP" ]] && ls "$SKILLS_TMP"/*/SKILL.md >/dev/null 2>&1; then
+    for skill_dir in "$SKILLS_TMP/"*/; do
       skill_name="$(basename "$skill_dir")"
       src="$skill_dir/SKILL.md"
       dst="$VAULT_DIR/.claude/skills/$skill_name/SKILL.md"
@@ -96,6 +96,11 @@ if [[ -d "$REPO_DIR/skills" ]]; then
     done
   fi
 
+  rm -rf "$SKILLS_TMP"
+else
+  warn "python3 not found — skipped skills update"
+fi
+
 # ── Update CLAUDE.md ──────────────────────────────────────────────────────
 CLAUDE_MD_UPDATED=""
 if [[ -f "$REPO_DIR/CLAUDE.md" ]]; then