cortexhawk 3.1.1 → 3.3.0

package/install.sh

@@ -7,7 +7,24 @@ SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 if [ -f ".env" ]; then
     while IFS='=' read -r key value; do
         [[ -z "$key" || "$key" == \#* ]] && continue
+        # Validate key format: uppercase letters, digits, underscore only (POSIX env var names)
+        [[ "$key" =~ ^[A-Z_][A-Z0-9_]{0,63}$ ]] || continue
+        # Block dangerous variable names that could hijack script/shell behavior
+        case "$key" in
+            PATH|LD_PRELOAD|LD_LIBRARY_PATH|LD_AUDIT|LD_DEBUG|BASH_ENV|BASH_FUNC_*|\
+            SCRIPT_DIR|HOME|SHELL|IFS|CDPATH|ENV|PYTHONPATH|PYTHONSTARTUP|\
+            GIT_SSH|GIT_SSH_COMMAND|GIT_PROXY_COMMAND|GIT_EXEC_PATH|\
+            NPM_CONFIG_*|NODE_OPTIONS|RUBYLIB|RUBYOPT|PERL5LIB|PERL5OPT)
+                continue ;;
+        esac
+        # Strip double quotes
         value="${value%\"}" && value="${value#\"}"
+        # Strip single quotes
+        value="${value%'}" && value="${value#'}"
+        # Strip inline comments (space + # marks start of comment)
+        value="$(printf '%s\n' "$value" | sed 's/[[:space:]]#.*$//')"
+        # Strip trailing whitespace
+        value="${value%"${value##*[! ]}"}"
         export "$key=$value" 2>/dev/null || true
     done < .env
 fi
@@ -20,6 +37,15 @@ get_version() {
     grep -m1 '## \[' "$SCRIPT_DIR/CHANGELOG.md" | sed 's/.*\[\([^]]*\)\].*/\1/'
 }
 
+# Portable sed -i (GNU vs BSD)
+sed_inplace() {
+    if sed --version 2>/dev/null | grep -q GNU; then
+        sed -i "$@"
+    else
+        sed -i '' "$@"
+    fi
+}
+
 compute_checksum() {
     local file="$1"
     if command -v sha256sum >/dev/null 2>&1; then
@@ -106,6 +132,7 @@ print_usage() {
     echo "  --dry-run         Simulate install/update without writing files"
     echo "  --test-hooks      Dry-run all hooks with synthetic inputs"
     echo "  --no-scan         Skip post-install security audit"
+    echo "  --version, -v     Show CortexHawk version"
     echo "  --help, -h        Show this help"
 }
 
@@ -144,15 +171,41 @@ STATS_MODE=false
 PUBLISH_SKILL_PATH=""
 CHECK_UPDATE_MODE=false
 DEMO_MODE=false
+TRUST_SKILL=false
 MAX_SNAPSHOTS=10
 
+# === Component Registry ===
+# Single source of truth for all CortexHawk components.
+# Format: "name:executable"
+#   - executable = "yes" runs chmod +x *.sh after copy (hooks, scripts)
+#   - executable = "no" for markdown-only components (agents, commands, modes)
+#   - skills handled specially via copy_skills()/sync_skills_update() for profile filtering
+# Used by: copy_all_components(), sync_all_components(), count_component_files()
+COMPONENTS=(
+    "agents:no"
+    "commands:no"
+    "skills:no"
+    "hooks:yes"
+    "modes:no"
+    "mcp:no"
+    "scripts:yes"
+)
+
 while [ $# -gt 0 ]; do
     case "$1" in
         --target)
+            if [ -z "${2:-}" ]; then
+                echo "Error: --target requires a value (claude|kimi|codex|auto|all)"
+                exit 1
+            fi
             TARGET_CLI="$2"
             shift 2
             ;;
         --profile)
+            if [ -z "${2:-}" ]; then
+                echo "Error: --profile requires a value (fullstack|api|data)"
+                exit 1
+            fi
             PROFILE="$2"
             shift 2
             ;;
@@ -218,6 +271,10 @@ while [ $# -gt 0 ]; do
             ;;
         --restore)
             RESTORE_MODE=true
+            if [ -z "${2:-}" ]; then
+                echo "Error: --restore requires a snapshot path or --latest"
+                exit 1
+            fi
             SNAPSHOT_FILE="$2"
             if [ "$SNAPSHOT_FILE" = "--latest" ]; then
                 if [ "$GLOBAL" = true ]; then
@@ -271,6 +328,10 @@ while [ $# -gt 0 ]; do
             DEMO_MODE=true
             shift
             ;;
+        --trust)
+            TRUST_SKILL=true
+            shift
+            ;;
         --publish-skill)
             PUBLISH_SKILL_PATH="$2"
             if [ -z "$PUBLISH_SKILL_PATH" ]; then
@@ -323,6 +384,10 @@ while [ $# -gt 0 ]; do
             fi
             shift 2
             ;;
+        --version|-v)
+            echo "CortexHawk $(get_version)"
+            exit 0
+            ;;
         --help|-h)
             print_usage
             exit 0
@@ -368,14 +433,6 @@ if [ "$RESTORE_MODE" = true ] && { [ "$INIT_MODE" = true ] || [ "$UPDATE_MODE" =
     echo "Error: --restore cannot be combined with --init or --update"
     exit 1
 fi
-if [ "$TARGET_CLI" = "all" ] && [ "$INIT_MODE" = true ]; then
-    echo "Error: --target all cannot be combined with --init (run --init per target instead)"
-    exit 1
-fi
-if [ "$TARGET_CLI" = "auto" ] && [ "$INIT_MODE" = true ]; then
-    echo "Error: --target auto cannot be combined with --init (run --init per target instead)"
-    exit 1
-fi
 if [ -n "$ADD_SKILL_URL" ] && { [ "$INIT_MODE" = true ] || [ "$UPDATE_MODE" = true ] || [ "$SNAPSHOT_MODE" = true ] || [ "$RESTORE_MODE" = true ]; }; then
     echo "Error: --add-skill cannot be combined with --init, --update, --snapshot, or --restore"
     exit 1
@@ -430,7 +487,7 @@ if [ -n "$PACK_NAME" ]; then
         exit 1
     fi
     _skills_csv=$(echo "$_row" | awk -F'|' '{print $3}' | sed 's/^ *//;s/ *$//')
-    _description=$(echo "$_row" | awk -F'|' '{print $4}' | sed 's/^ *//;s/ *$//')
+    _description=$(echo "$_row" | awk -F'|' '{print $4}' | sed 's/^ *//;s/ *$//' | sed 's/"/\\"/g')
     _tmp_profile=$(mktemp /tmp/cortexhawk-pack-XXXXXX.json)
     {
         echo '{'
@@ -480,12 +537,17 @@ detect_installed_clis() {
 copy_skills() {
     local target_dir="$1"
     local profile="$2"
+    local source_dir="${3:-$SCRIPT_DIR}"
     if [ -z "$profile" ]; then
-        cp -r "$SCRIPT_DIR/skills/"* "$target_dir/skills/" 2>/dev/null || true
+        cp -r "$source_dir/skills/"* "$target_dir/skills/" 2>/dev/null || true
     else
         grep '"[a-z]' "$PROFILE_FILE" | sed 's/.*"\([a-z][^"]*\)".*/\1/' | grep '/' | while read -r skill; do
-            local src="$SCRIPT_DIR/skills/$skill"
+            local src="$source_dir/skills/$skill"
             local dest="$target_dir/skills/$skill"
+            if [ ! -d "$src" ]; then
+                yellow "  Warning: skill '$skill' not found in source — skipping"
+                continue
+            fi
             mkdir -p "$(dirname "$dest")"
             cp -r "$src" "$dest" 2>/dev/null || true
         done
@@ -545,6 +607,9 @@ convert_modes_to_skills() {
     done
 }
 
+# NOTE: profiles/*.json contain an "mcp" field listing recommended servers, but install.sh
+# currently installs all mcp/*.json regardless of profile. Per-profile MCP filtering is planned
+# for a future phase of #137 (install.sh modularization).
 # merge_mcp_json(output_file) — merges mcp/*.json into single JSON file
 merge_mcp_json() {
     local output_file="$1"
@@ -553,7 +618,7 @@ merge_mcp_json() {
         [ -f "$mcp_file" ] || continue
         local server_name command_val args_val entry
         server_name=$(basename "$mcp_file" .json)
-        command_val=$(grep '"command"' "$mcp_file" | sed 's/.*"command"[[:space:]]*:[[:space:]]*"\([^"]*\)".*/\1/')
+        command_val=$(grep '"command"' "$mcp_file" | sed 's/.*"command"[[:space:]]*:[[:space:]]*"\([^"]*\)".*/\1/' | sed 's/"/\\"/g')
         args_val=$(grep '"args"' "$mcp_file" | sed 's/.*"args"[[:space:]]*:[[:space:]]*\(\[.*\]\).*/\1/')
         entry="    \"$server_name\": {\n      \"command\": \"$command_val\",\n      \"args\": $args_val\n    }"
         if [ -n "$entries" ]; then
@@ -594,11 +659,34 @@ update_gitignore() {
         touch "$gitignore"
     fi
 
-    # Auto-add target directory (always)
-    if ! grep -qx "$target_dir/" "$gitignore" 2>/dev/null; then
-        echo "" >> "$gitignore"
-        echo "# CortexHawk" >> "$gitignore"
-        echo "$target_dir/" >> "$gitignore"
+    # Ensure essential entries are present (disable glob to keep *.log literal)
+    local essentials="node_modules/ __pycache__/ .env .env.local *.log dist/ build/ .DS_Store"
+    local added_count=0
+    set -f
+    for entry in $essentials; do
+        if ! grep -qxF "$entry" "$gitignore" 2>/dev/null; then
+            echo "$entry" >> "$gitignore"
+            added_count=$((added_count + 1))
+        fi
+    done
+    set +f
+    if [ "$added_count" -gt 0 ]; then
+        green "  Added $added_count essential entries to .gitignore (.env, node_modules/, etc.)"
+    fi
+
+    # Auto-add target directory (always), group under single header
+    if ! grep -qxF "$target_dir/" "$gitignore" 2>/dev/null; then
+        if grep -q "# CortexHawk" "$gitignore" 2>/dev/null; then
+            # Append under the first existing header only
+            local header_line
+            header_line=$(grep -n "# CortexHawk" "$gitignore" | head -1 | cut -d: -f1)
+            sed_inplace "${header_line}a\\
+$target_dir/" "$gitignore"
+        else
+            echo "" >> "$gitignore"
+            echo "# CortexHawk" >> "$gitignore"
+            echo "$target_dir/" >> "$gitignore"
+        fi
         green "  Added $target_dir/ to .gitignore"
     fi
 
@@ -606,19 +694,69 @@ update_gitignore() {
     if [ -d "$project_root/docs" ] && ! grep -qx "docs/" "$gitignore" 2>/dev/null; then
         echo ""
         echo "  docs/ contains agent outputs (brainstorms, plans, research)."
-        read -r -p "  Track docs/ in git? [Y/n]: " docs_choice
+        if [ -t 0 ]; then
+            read -r -p "  Track docs/ in git? [Y/n]: " docs_choice
+        else
+            docs_choice="Y"
+        fi
         case "$docs_choice" in
             [nN]*)
                 echo "docs/" >> "$gitignore"
                 green "  Added docs/ to .gitignore"
                 ;;
             *)
-                green "  docs/ will be tracked in git"
+                green "  docs/ will be tracked in git (default)"
                 ;;
         esac
     fi
 }
 
+# --- setup_templates() ---
+# Detects existing PR/commit templates; generates CortexHawk defaults if missing
+# Args: $1=project_root
+setup_templates() {
+    local project_root="$1"
+
+    [ "$GLOBAL" = true ] && return
+
+    # PR template
+    local pr_template=""
+    for path in ".github/PULL_REQUEST_TEMPLATE.md" ".github/pull_request_template.md" "docs/pull_request_template.md"; do
+        if [ -f "$project_root/$path" ]; then
+            pr_template="$path"
+            break
+        fi
+    done
+    # Also check template directory
+    if [ -z "$pr_template" ] && [ -d "$project_root/.github/PULL_REQUEST_TEMPLATE" ]; then
+        pr_template=".github/PULL_REQUEST_TEMPLATE/"
+    fi
+
+    if [ -n "$pr_template" ]; then
+        green "  PR template found: $pr_template"
+    else
+        mkdir -p "$project_root/.github"
+        cp "$SCRIPT_DIR/templates/github/PULL_REQUEST_TEMPLATE.md" "$project_root/.github/PULL_REQUEST_TEMPLATE.md"
+        green "  PR template created: .github/PULL_REQUEST_TEMPLATE.md"
+    fi
+
+    # Commit template
+    local commit_template=""
+    for path in ".gitmessage" ".github/gitmessage" ".github/commit-template"; do
+        if [ -f "$project_root/$path" ]; then
+            commit_template="$path"
+            break
+        fi
+    done
+
+    if [ -n "$commit_template" ]; then
+        green "  Commit template found: $commit_template"
+    else
+        cp "$SCRIPT_DIR/templates/github/gitmessage" "$project_root/.gitmessage"
+        green "  Commit template created: .gitmessage"
+    fi
+}
+
 # --- run_audit() ---
 run_audit() {
     local project_root="$1"
@@ -641,11 +779,12 @@ generate_hooks_config() {
     fi
 
     if ! command -v python3 >/dev/null 2>&1; then
+        yellow "  Warning: python3 not found — hooks config will use static fallback" >&2
         return 1
     fi
 
-    python3 << PYEOF
-import re, json, sys
+    python3 - "$compose_file" "$hooks_dir" << 'PYEOF'
+import re, json, sys, shlex
 
 def parse_compose(path, hooks_dir):
     """Parse compose.yml and generate Claude Code hooks JSON."""
@@ -679,10 +818,13 @@ def parse_compose(path, hooks_dir):
         # Hook item
         elif line.strip().startswith('- '):
             hook_name = line.strip()[2:].strip()
+            if not re.match(r'^[a-zA-Z0-9_-]+$', hook_name):
+                print(f"Warning: skipping invalid hook name: {hook_name}", file=sys.stderr)
+                continue
             hook_path = f"{hooks_dir}/{hook_name}.sh"
 
             # Build command — hooks read stdin JSON (Claude Code protocol)
-            cmd = f'bash {hook_path}'
+            cmd = f'bash {shlex.quote(hook_path)}'
 
             hook_entry = {"type": "command", "command": cmd}
 
@@ -708,7 +850,7 @@ def parse_compose(path, hooks_dir):
     return result
 
 try:
-    result = parse_compose("$compose_file", "$hooks_dir")
+    result = parse_compose(sys.argv[1], sys.argv[2])
     print(json.dumps(result, indent=2))
 except Exception as e:
     print(f"Error: {e}", file=sys.stderr)
@@ -786,7 +928,8 @@ update_source_git() {
 }
 
 update_source_release() {
-    local tmp_dir="/tmp/cortexhawk-update-$$"
+    local tmp_dir
+    tmp_dir=$(mktemp -d /tmp/cortexhawk-update-XXXXXX)
     local repo_url
     repo_url=$(get_source_url)
     if [ -z "$repo_url" ] && [ -f "$TARGET/.cortexhawk-manifest" ]; then
@@ -797,13 +940,19 @@ update_source_release() {
         echo "Set CORTEXHAWK_REPO environment variable and retry"
         exit 1
     fi
-    mkdir -p "$tmp_dir"
     echo "  Downloading from $repo_url..."
-    if ! curl -sL "$repo_url/archive/refs/heads/main.tar.gz" | tar xz -C "$tmp_dir" --strip-components=1; then
+    local tarball="$tmp_dir/update.tar.gz"
+    if ! curl -sL "$repo_url/archive/refs/heads/main.tar.gz" -o "$tarball"; then
         echo "Error: failed to download latest release"
         rm -rf "$tmp_dir"
         exit 1
     fi
+    if ! tar xzf "$tarball" -C "$tmp_dir" --strip-components=1; then
+        echo "Error: failed to extract update archive"
+        rm -rf "$tmp_dir"
+        exit 1
+    fi
+    rm -f "$tarball"
     SCRIPT_DIR="$tmp_dir"
     UPDATE_CLEANUP_DIR="$tmp_dir"
 }
@@ -995,6 +1144,48 @@ sync_skills_update() {
     fi
 }
 
+# === Generic Component Operations ===
+# These use the COMPONENTS array to avoid hardcoding directory lists.
+
+# copy_all_components(source_dir, target_dir, profile)
+copy_all_components() {
+    local src="$1" dst="$2" profile="$3"
+    for entry in "${COMPONENTS[@]}"; do
+        IFS=':' read -r name exec_flag <<< "$entry"
+        [ -d "$src/$name" ] || continue
+        mkdir -p "$dst/$name"
+        if [ "$name" = "skills" ] && [ -n "$profile" ]; then
+            copy_skills "$dst" "$profile" "$src"
+        else
+            cp -r "$src/$name/"* "$dst/$name/" 2>/dev/null || true
+        fi
+        [ "$exec_flag" = "yes" ] && chmod +x "$dst/$name/"*.sh 2>/dev/null || true
+    done
+}
+
+# sync_all_components(profile)
+sync_all_components() {
+    local profile="$1"
+    for entry in "${COMPONENTS[@]}"; do
+        IFS=':' read -r name exec_flag <<< "$entry"
+        if [ "$name" = "skills" ]; then
+            sync_skills_update "$profile"
+        else
+            sync_component "$name"
+        fi
+    done
+}
+
+# count_component_files(source_dir)
+count_component_files() {
+    local src="$1"
+    for entry in "${COMPONENTS[@]}"; do
+        IFS=':' read -r name _ <<< "$entry"
+        local c; c=$(find "$src/$name" -type f 2>/dev/null | wc -l | tr -d ' ')
+        printf "  %-12s %s files\n" "$name/" "$c"
+    done
+}
+
 do_update() {
     # 1. Validate target
     if [ "$TARGET_CLI" != "claude" ]; then
@@ -1143,12 +1334,7 @@ do_update() {
     SYNC_SKIPPED=0
     SYNC_CONFLICTS=0
 
-    sync_component "agents"
-    sync_component "commands"
-    sync_skills_update "$update_profile"
-    sync_component "hooks"
-    sync_component "modes"
-    sync_component "mcp"
+    sync_all_components "$update_profile"
 
     # 6b. Sync agent personas from project root
     local project_root
@@ -1173,33 +1359,46 @@ do_update() {
     fi
 
     if [ "$DRY_RUN" != true ]; then
-        # Make hooks executable
-        chmod +x "$TARGET/hooks/"*.sh 2>/dev/null || true
+        # Make executable components executable
+        for entry in "${COMPONENTS[@]}"; do
+            IFS=':' read -r name exec_flag <<< "$entry"
+            [ "$exec_flag" = "yes" ] && chmod +x "$TARGET/$name/"*.sh 2>/dev/null || true
+        done
 
-        # 7b. Regenerate settings.json hooks section from compose.yml
+        # 7b. Regenerate settings.json hooks + merge new permissions from compose.yml
         if [ -f "$SCRIPT_DIR/hooks/compose.yml" ]; then
             local hooks_json
             hooks_json=$(generate_hooks_config "$SCRIPT_DIR/hooks/compose.yml" ".claude/hooks")
-            if [ -n "$hooks_json" ]; then
-                python3 << PYEOF
+            if [ -n "$hooks_json" ] && [ "$hooks_json" != "{}" ]; then
+                echo "$hooks_json" | python3 -c "
 import json, sys
-
-# Read current settings.json to preserve permissions
+hooks = json.load(sys.stdin)
 current = {}
 try:
-    with open('$TARGET/settings.json') as f:
+    with open(sys.argv[1]) as f:
         current = json.load(f)
 except:
     pass
-
-# Merge: keep existing permissions, replace hooks
-hooks = json.loads('''$hooks_json''')
 current['hooks'] = hooks
-
-with open('$TARGET/settings.json', 'w') as f:
+# Merge new permissions from source
+try:
+    with open(sys.argv[2]) as f:
+        src_perms = json.load(f).get('permissions', {})
+    cur_perms = current.get('permissions', {})
+    for key in ('allow', 'deny'):
+        src_list = src_perms.get(key, [])
+        cur_list = cur_perms.get(key, [])
+        added = [p for p in src_list if p not in cur_list]
+        if added:
+            cur_list.extend(added)
+        cur_perms[key] = cur_list
+    current['permissions'] = cur_perms
+except:
+    pass
+with open(sys.argv[1], 'w') as f:
     json.dump(current, f, indent=2)
     f.write('\n')
-PYEOF
+" "$TARGET/settings.json" "$SCRIPT_DIR/settings.json"
                 echo "  Regenerated settings.json hooks from compose.yml"
             fi
         fi
@@ -1214,6 +1413,7 @@ PYEOF
         local target_dir_name=".${TARGET_CLI:-claude}"
         update_gitignore "$(dirname "$TARGET")" "$target_dir_name"
         [ "$TARGET_CLI" = "codex" ] && update_gitignore "$(dirname "$TARGET")" ".agents"
+        setup_templates "$(dirname "$TARGET")"
 
         if [ ! -f "$TARGET/git-workflow.conf" ]; then
             GIT_BRANCHING="direct-main"
@@ -1313,12 +1513,10 @@ do_snapshot() {
         git_push=$(grep '^AUTO_PUSH=' "$TARGET/git-workflow.conf" | cut -d= -f2)
     fi
 
-    # Read custom profile if applicable
+    # Read custom profile if applicable (use PROFILE_FILE from current run, never glob /tmp/)
     local profile_def="null"
-    local custom_profile
-    custom_profile=$(ls /tmp/cortexhawk-custom-*.json 2>/dev/null | head -1)
-    if [ -n "$custom_profile" ] && [ -f "$custom_profile" ]; then
-        profile_def=$(cat "$custom_profile")
+    if [ -n "$PROFILE_FILE" ] && [ -f "$PROFILE_FILE" ]; then
+        profile_def=$(cat "$PROFILE_FILE")
     fi
 
     # Build files checksums from manifest
@@ -1369,7 +1567,7 @@ do_snapshot() {
     [ -n "$git_workflow_content" ] && printf '    "git-workflow.conf": "%s",\n' "$git_workflow_content" >> "$snap_file"
     [ -n "$claude_md_content" ] && printf '    "CLAUDE.md": "%s",\n' "$claude_md_content" >> "$snap_file"
     # Remove trailing comma from last entry
-    sed -i '$ s/,$//' "$snap_file"
+    sed_inplace '$ s/,$//' "$snap_file"
     printf '  }\n' >> "$snap_file"
     printf '}\n' >> "$snap_file"
 
@@ -1850,40 +2048,28 @@ do_restore() {
 
     # Reinstall using the standard flow
     echo "Reinstalling CortexHawk components..."
-    mkdir -p "$TARGET"/{agents,commands,skills,hooks,modes,mcp}
 
     # Use portable archive files if available, otherwise use source repo
     if [ -n "$portable_files" ] && [ -d "$portable_files" ]; then
         echo "  Using files from portable archive..."
-        cp -r "$portable_files/agents/"* "$TARGET/agents/" 2>/dev/null || true
-        cp -r "$portable_files/commands/"* "$TARGET/commands/" 2>/dev/null || true
-        cp -r "$portable_files/skills/"* "$TARGET/skills/" 2>/dev/null || true
-        cp -r "$portable_files/hooks/"* "$TARGET/hooks/" 2>/dev/null || true
-        cp -r "$portable_files/modes/"* "$TARGET/modes/" 2>/dev/null || true
-        cp -r "$portable_files/mcp/"* "$TARGET/mcp/" 2>/dev/null || true
+        copy_all_components "$portable_files" "$TARGET" ""
     else
-        cp -r "$SCRIPT_DIR/agents/"* "$TARGET/agents/" 2>/dev/null || true
-        cp -r "$SCRIPT_DIR/commands/"* "$TARGET/commands/" 2>/dev/null || true
-        copy_skills "$TARGET" "$PROFILE"
-        cp -r "$SCRIPT_DIR/hooks/"* "$TARGET/hooks/" 2>/dev/null || true
-        cp -r "$SCRIPT_DIR/modes/"* "$TARGET/modes/" 2>/dev/null || true
-        cp -r "$SCRIPT_DIR/mcp/"* "$TARGET/mcp/" 2>/dev/null || true
+        copy_all_components "$SCRIPT_DIR" "$TARGET" "$PROFILE"
     fi
-    chmod +x "$TARGET/hooks/"*.sh 2>/dev/null || true
 
     # Restore settings.json from snapshot
     if command -v python3 >/dev/null 2>&1; then
         python3 -c "
 import json, sys
-with open('$snap_file') as f:
+with open(sys.argv[1]) as f:
     snap = json.load(f)
 settings = snap.get('settings')
 if settings is not None:
-    with open('$TARGET/settings.json', 'w') as f:
+    with open(sys.argv[2], 'w') as f:
         json.dump(settings, f, indent=2)
         f.write('\n')
     print('  Restored settings.json')
-"
+" "$snap_file" "$TARGET/settings.json"
     else
         echo "  Warning: python3 not found — settings.json not restored from snapshot"
     fi
@@ -1909,23 +2095,24 @@ if settings is not None:
     if grep -q '"file_contents"' "$snap_file" && command -v python3 >/dev/null 2>&1; then
         python3 -c "
 import json, base64, sys, os
-with open('$snap_file') as f:
+snap_file, target_dir = sys.argv[1], sys.argv[2]
+with open(snap_file) as f:
     snap = json.load(f)
 contents = snap.get('file_contents', {})
 for filename, b64data in contents.items():
     try:
         data = base64.b64decode(b64data).decode('utf-8')
         if filename == 'CLAUDE.md':
-            target_path = os.path.dirname('$TARGET') + '/CLAUDE.md'
+            target_path = os.path.dirname(target_dir) + '/CLAUDE.md'
         else:
-            target_path = '$TARGET/' + filename
+            target_path = target_dir + '/' + filename
         os.makedirs(os.path.dirname(target_path), exist_ok=True)
         with open(target_path, 'w') as f:
             f.write(data)
         print(f'  Restored {filename} (from file_contents)')
     except Exception as e:
         print(f'  Warning: could not restore {filename}: {e}', file=sys.stderr)
-"
+" "$snap_file" "$TARGET"
     fi
 
     # Write new manifest
@@ -2312,14 +2499,14 @@ do_list_hooks() {
     printf "  %-20s %-14s %-8s %s\n" "Name" "Event" "Status" "Description"
     printf "  %-20s %-14s %-8s %s\n" "----" "-----" "------" "-----------"
     # Parse hooks.json with python3 for reliable JSON handling
-    python3 << PYEOF
-import json
-with open("$hooks_json") as f:
+    python3 - "$hooks_json" "$compose_file" << 'PYEOF'
+import json, sys
+with open(sys.argv[1]) as f:
     data = json.load(f)
 # Read compose.yml to detect disabled hooks (commented out)
 disabled = set()
 try:
-    with open("$compose_file") as f:
+    with open(sys.argv[2]) as f:
         for line in f:
             stripped = line.strip()
             if stripped.startswith("# - "):
@@ -2368,14 +2555,14 @@ do_toggle_hook() {
             echo "Hook '$hook_name' is already disabled"
             return 0
         fi
-        sed -i "s/^      - ${hook_name}$/      # - ${hook_name}/" "$compose_file"
+        sed_inplace "s/^      - ${hook_name}$/      # - ${hook_name}/" "$compose_file"
         echo "Disabled hook: $hook_name"
     else
         if grep -q "^      - ${hook_name}$" "$compose_file"; then
             echo "Hook '$hook_name' is already enabled"
             return 0
         fi
-        sed -i "s/^      # - ${hook_name}$/      - ${hook_name}/" "$compose_file"
+        sed_inplace "s/^      # - ${hook_name}$/      - ${hook_name}/" "$compose_file"
         echo "Enabled hook: $hook_name"
     fi
     # Regenerate settings.json if target exists
@@ -2383,17 +2570,18 @@ do_toggle_hook() {
     if [ -d "$target" ] && [ -f "$target/settings.json" ]; then
         local hooks_json
         hooks_json=$(generate_hooks_config "$compose_file" ".claude/hooks")
-        if [ -n "$hooks_json" ]; then
-            python3 << PYEOF
-import json
-with open('$target/settings.json') as f:
+        if [ -n "$hooks_json" ] && [ "$hooks_json" != "{}" ]; then
+            echo "$hooks_json" | python3 -c "
+import json, sys
+hooks = json.load(sys.stdin)
+with open(sys.argv[1]) as f:
     settings = json.load(f)
-settings['hooks'] = json.loads('''$hooks_json''')
-with open('$target/settings.json', 'w') as f:
+settings['hooks'] = hooks
+with open(sys.argv[1], 'w') as f:
     json.dump(settings, f, indent=2)
     f.write('\n')
 print('  Regenerated settings.json')
-PYEOF
+" "$target/settings.json"
         fi
     fi
 }
@@ -2441,17 +2629,18 @@ _search_skillsmp() {
     fi
 
     # Parse JSON response with python3
-    python3 << PYEOF
+    python3 - "$tmp_response" "$keyword" << 'PYEOF'
 import json, sys
 try:
-    with open("$tmp_response") as f:
+    response_file, keyword = sys.argv[1], sys.argv[2]
+    with open(response_file) as f:
         data = json.load(f)
     container = data.get("data", {})
     skills = container.get("skills", [])
     pagination = container.get("pagination", {})
     total = pagination.get("total", len(skills))
     if not skills:
-        print("  No skills found matching '$keyword'")
+        print(f"  No skills found matching '{keyword}'")
         print("")
         print("  Try broader terms or check https://skillsmp.com")
         sys.exit(0)
@@ -2474,7 +2663,7 @@ try:
             if len(parts) >= 2:
                 print(f"  Install: ./install.sh --add-skill {parts[0]}/{parts[1]}")
                 break
-    print(f"  Browse all: https://skillsmp.com/?q=$keyword")
+    print(f"  Browse all: https://skillsmp.com/?q={keyword}")
 except Exception as e:
     print(f"  Error parsing response: {e}")
     print("  Falling back to local registry")
@@ -2593,10 +2782,17 @@ do_add_skill() {
         exit 1
     fi
 
-    # Security warning if scripts present
+    # Security gate: block skills with executable scripts unless --trust is used
     if find "$tmp_dir/repo" -name "*.sh" -o -name "*.py" 2>/dev/null | grep -q .; then
-        echo "  Warning: this skill contains executable scripts"
-        echo "  Review them before use: $skill_dir/scripts/"
+        if [ "${TRUST_SKILL:-false}" = true ]; then
+            yellow "  Warning: this skill contains executable scripts — installing with --trust"
+        else
+            echo "  ERROR: This skill contains executable scripts (.sh/.py)."
+            echo "  Re-run with --trust to install: install.sh --add-skill $ADD_SKILL_URL --trust"
+            echo "  Review the source first: $ADD_SKILL_URL"
+            rm -rf "$tmp_dir"
+            exit 1
+        fi
     fi
 
     # Create community directory if needed
@@ -2717,7 +2913,8 @@ do_team_install() {
 
     # Generate temporary profile JSON from skills list
     if [ -n "$TEAM_SKILLS" ]; then
-        local tmp_profile="/tmp/cortexhawk-team-$$.json"
+        local tmp_profile
+        tmp_profile=$(mktemp /tmp/cortexhawk-team-XXXXXX.json)
         printf '{\n  "name": "team",\n  "skills": [\n' > "$tmp_profile"
         local first=true
         while IFS= read -r skill; do
@@ -2808,12 +3005,7 @@ install_claude() {
         echo "  Profile: ${PROFILE:-all}"
         echo ""
         echo "Would install:"
-        for comp in agents commands hooks modes mcp; do
-            local c; c=$(find "$SCRIPT_DIR/$comp" -type f 2>/dev/null | wc -l | tr -d ' ')
-            printf "  %-12s %s files\n" "$comp/" "$c"
-        done
-        local sc; sc=$(find "$SCRIPT_DIR/skills" -type f 2>/dev/null | wc -l | tr -d ' ')
-        printf "  %-12s %s files\n" "skills/" "$sc"
+        count_component_files "$SCRIPT_DIR"
         echo "  settings.json"
         [ ! -f "$(pwd)/CLAUDE.md" ] && echo "  CLAUDE.md"
         echo ""
@@ -2823,9 +3015,8 @@ install_claude() {
 
     echo "Installing for Claude Code to project: $TARGET"
 
-    mkdir -p "$TARGET"/{agents,commands,skills,hooks,modes,mcp}
+    copy_all_components "$SCRIPT_DIR" "$TARGET" "$PROFILE"
 
-    cp -r "$SCRIPT_DIR/agents/"* "$TARGET/agents/" 2>/dev/null || true
     # Copy agent personas from project root if present
     local project_root
     project_root="$(dirname "$TARGET")"
@@ -2835,32 +3026,79 @@ install_claude() {
         persona_count=$(find "$project_root/.cortexhawk-agents" -name "*.md" -type f 2>/dev/null | wc -l | tr -d ' ')
         [ "$persona_count" -gt 0 ] && echo "  Loaded $persona_count agent persona(s) from .cortexhawk-agents/"
     fi
-    cp -r "$SCRIPT_DIR/commands/"* "$TARGET/commands/" 2>/dev/null || true
-    copy_skills "$TARGET" "$PROFILE"
-    cp -r "$SCRIPT_DIR/hooks/"* "$TARGET/hooks/" 2>/dev/null || true
-    cp -r "$SCRIPT_DIR/modes/"* "$TARGET/modes/" 2>/dev/null || true
-    cp -r "$SCRIPT_DIR/mcp/"* "$TARGET/mcp/" 2>/dev/null || true
 
+    local hooks_json
+    hooks_json=$(generate_hooks_config "$SCRIPT_DIR/hooks/compose.yml" ".claude/hooks")
     if [ ! -f "$TARGET/settings.json" ]; then
-        # Generate settings.json with hooks from compose.yml
-        local hooks_json
-        hooks_json=$(generate_hooks_config "$SCRIPT_DIR/hooks/compose.yml" ".claude/hooks")
+        # Fresh install: generate settings.json from scratch
         if [ -n "$hooks_json" ] && [ "$hooks_json" != "{}" ]; then
-            # Build settings.json with generated hooks
-            python3 -c "
-import json
-permissions = $(cat "$SCRIPT_DIR/settings.json" | python3 -c "import sys,json; d=json.load(sys.stdin); print(json.dumps(d.get('permissions',{})))")
-hooks = $hooks_json
-with open('$TARGET/settings.json', 'w') as f:
+            echo "$hooks_json" | python3 -c "
+import json, sys
+hooks = json.load(sys.stdin)
+with open(sys.argv[1]) as f:
+    permissions = json.load(f).get('permissions', {})
+with open(sys.argv[2], 'w') as f:
     json.dump({'permissions': permissions, 'hooks': hooks}, f, indent=2)
     f.write('\n')
-"
+" "$SCRIPT_DIR/settings.json" "$TARGET/settings.json"
             echo "  Generated settings.json from hooks/compose.yml"
         else
             cp "$SCRIPT_DIR/settings.json" "$TARGET/settings.json"
         fi
     else
-        echo "settings.json already exists — skipping (check manually for updates)"
+        # Merge: preserve user customizations, add new hooks + permissions
+        python3 -c "
+import json, sys, shutil, os
+
+raw = sys.stdin.read().strip()
+hooks = json.loads(raw) if raw else {}
+
+# Load current settings (tolerate corrupted JSON)
+try:
+    with open(sys.argv[1]) as f:
+        current = json.load(f)
+except Exception:
+    backup = sys.argv[1] + '.bak'
+    if os.path.isfile(sys.argv[1]):
+        shutil.copy2(sys.argv[1], backup)
+        print(f'  Warning: settings.json corrupted — backed up to {os.path.basename(backup)}', file=sys.stderr)
+    current = {}
+
+try:
+    with open(sys.argv[2]) as f:
+        source = json.load(f)
+except Exception:
+    source = {}
+
+changes = []
+
+# Merge hooks (regenerate from compose.yml)
+if hooks and hooks != {}:
+    current['hooks'] = hooks
+    changes.append('hooks regenerated')
+
+# Merge permissions (union: keep user additions + add new from source)
+src_perms = source.get('permissions', {})
+cur_perms = current.get('permissions', {})
+for key in ('allow', 'deny'):
+    src_list = src_perms.get(key, [])
+    cur_list = cur_perms.get(key, [])
+    added = [p for p in src_list if p not in cur_list]
+    if added:
+        cur_list.extend(added)
+        changes.append(f'{len(added)} new {key} permission(s)')
+    cur_perms[key] = cur_list
+current['permissions'] = cur_perms
+
+with open(sys.argv[1], 'w') as f:
+    json.dump(current, f, indent=2)
+    f.write('\n')
+
+if changes:
+    print('  Merged settings.json: ' + ', '.join(changes))
+else:
+    print('  settings.json up to date — no merge needed')
+" "$TARGET/settings.json" "$SCRIPT_DIR/settings.json" <<< "${hooks_json:-}"
     fi
 
     PROJECT_ROOT="$(dirname "$TARGET")"
@@ -2897,11 +3135,12 @@ with open('$TARGET/settings.json', 'w') as f:
 
     run_audit "$(dirname "$TARGET")"
     update_gitignore "$(dirname "$TARGET")" ".claude"
+    setup_templates "$(dirname "$TARGET")"
 
     echo ""
     echo "CortexHawk installed successfully for Claude Code!"
     echo ""
-    echo "  32 commands | 20 agents | 36 skills | 9 hooks | 7 modes"
+    echo "  33 commands | 20 agents | 36 skills | 9 hooks | 7 modes"
     echo ""
     do_quickstart
     echo ""
@@ -3163,7 +3402,8 @@ do_test_hooks() {
     echo ""
 
     local ok=0 fail=0
-    local tmpfile="/tmp/.cortexhawk-hooktest-$$"
+    local tmpfile
+    tmpfile=$(mktemp /tmp/.cortexhawk-hooktest-XXXXXX)
     echo "test file content" > "$tmpfile"
 
     for hook in "$hooks_dir"/*.sh; do
@@ -3501,9 +3741,11 @@ do_publish_skill() {
     # Create GitHub repo
     echo ""
     echo "  Creating repository..."
+    local repo_exists=false
     if gh repo view "$gh_user/$repo_name" &>/dev/null; then
         echo "  Repository already exists: $gh_user/$repo_name"
         echo "  Pushing latest files..."
+        repo_exists=true
     else
         gh repo create "$repo_name" --public --description "CortexHawk skill: $skill_desc" --clone=false
     fi
@@ -3527,7 +3769,11 @@ do_publish_skill() {
     git commit --quiet -m "feat: publish $skill_name skill"
     git branch -M main
     git remote add origin "https://github.com/$gh_user/$repo_name.git"
-    git push -u origin main --force --quiet 2>/dev/null
+    if [ "$repo_exists" = true ]; then
+        git push -u origin main --quiet 2>/dev/null
+    else
+        git push -u origin main --force --quiet 2>/dev/null
+    fi
     cd - >/dev/null
 
     # Cleanup
@@ -3562,7 +3808,8 @@ do_publish_skill() {
 
 # --- do_demo() ---
 do_demo() {
-    local demo_dir="/tmp/cortexhawk-demo-$$"
+    local demo_dir
+    demo_dir=$(mktemp -d /tmp/cortexhawk-demo-XXXXXX)
     mkdir -p "$demo_dir"
 
     echo ""
@@ -3749,7 +3996,6 @@ else
             install_codex
             ;;
         auto)
-            local detected
             detected=$(detect_installed_clis)
             if [ -z "$detected" ]; then
                 echo "Error: no supported CLI found (claude, kimi, codex)"
@@ -3758,7 +4004,7 @@ else
             fi
             echo "Auto-detected CLIs: $detected"
             echo ""
-            local auto_count=0
+            auto_count=0
             for cli in $detected; do
                 [ $auto_count -gt 0 ] && echo "" && echo "---" && echo ""
                 case "$cli" in