fix(upgrade): resolve 23 issues in make upgrade workflow

catalog/black.json

@@ -4,5 +4,6 @@
   "install_method": "uv_tool",
   "description": "The uncompromising Python code formatter",
   "homepage": "https://github.com/psf/black",
-  "package_name": "black"
+  "package_name": "black",
+  "version_command": "black --version 2>/dev/null | head -1"
 }

catalog/flake8.json

@@ -4,5 +4,6 @@
   "install_method": "uv_tool",
   "description": "Python style guide enforcement tool combining PyFlakes, pycodestyle, and McCabe complexity checker",
   "homepage": "https://github.com/PyCQA/flake8",
-  "package_name": "flake8"
+  "package_name": "flake8",
+  "version_command": "flake8 --version 2>/dev/null | head -1"
 }

catalog/gam.json

@@ -7,6 +7,8 @@
   "github_repo": "GAM-team/GAM",
   "binary_name": "gam",
   "version_flag": "version",
+  "version_command": "gam version 2>/dev/null | head -1 | grep -oE 'GAM [0-9]+\\.[0-9]+\\.[0-9]+' | awk '{print $2}'",
+  "version_regex": "([0-9]+\\.[0-9]+\\.[0-9]+)",
   "package_name": "gam7",
   "auto_update": true
 }

catalog/gcloud.json

@@ -6,5 +6,6 @@
   "homepage": "https://cloud.google.com/sdk/gcloud",
   "binary_name": "gcloud",
   "skip_upstream": true,
+  "version_command": "gcloud version 2>/dev/null | head -1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'",
   "notes": "Installed via Google Cloud SDK installer; self-updates with 'gcloud components update'"
 }

catalog/isort.json

@@ -4,5 +4,6 @@
   "install_method": "uv_tool",
   "description": "A Python utility to sort imports alphabetically and automatically separate them into sections",
   "homepage": "https://github.com/PyCQA/isort",
-  "package_name": "isort"
+  "package_name": "isort",
+  "version_command": "isort --version-number 2>/dev/null"
 }

catalog/pip.json

@@ -1,16 +1,11 @@
 {
   "name": "pip",
   "category": "python",
-  "install_method": "package_manager",
+  "install_method": "dedicated_script",
   "description": "Python package installer",
   "homepage": "https://pip.pypa.io/",
   "package_name": "pip",
   "binary_name": "pip",
-  "packages": {
-    "apt": "python3-pip",
-    "brew": "python3",
-    "dnf": "python3-pip",
-    "pacman": "python-pip"
-  },
-  "notes": "pip typically comes with Python 3. Use python3 -m pip if pip command is not available."
+  "script": "install_pip.sh",
+  "notes": "pip is bundled with Python 3. Use python3 -m pip if pip command is not available."
 }

scripts/guide.sh

@@ -1,16 +1,42 @@
 #!/usr/bin/env bash
 set -euo pipefail
 trap '' PIPE
+# Graceful interrupt handling
+INTERRUPTED=0
+trap 'INTERRUPTED=1; echo; echo "⚠️  Interrupted. Partial summary:"; print_summary; exit 130' INT
 
 DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 ROOT="$(cd "$DIR/.." && pwd)"
 VERBOSE="${VERBOSE:-0}"
+# Suppress Homebrew auto-update during upgrade runs to reduce noise
+export HOMEBREW_NO_AUTO_UPDATE=1
 OFFLINE="${OFFLINE:-0}"
 CLI="${PYTHON:-python3}"
 
 # Ignore pins: IGNORE_PINS=1 to show all tools regardless of pin status
 IGNORE_PINS="${IGNORE_PINS:-0}"
 
+# Summary counters
+SUMMARY_UPDATED=0
+SUMMARY_INSTALLED=0
+SUMMARY_SKIPPED=0
+SUMMARY_FAILED=0
+SUMMARY_REMOVED=0
+
+print_summary() {
+  local label="${1:-interrupted}"
+  echo "================================================================================"
+  echo "Summary${label:+ ($label)}"
+  echo "================================================================================"
+  printf "  Installed: %d\n" "$SUMMARY_INSTALLED"
+  printf "  Updated:   %d\n" "$SUMMARY_UPDATED"
+  printf "  Removed:   %d\n" "$SUMMARY_REMOVED"
+  printf "  Skipped:   %d\n" "$SUMMARY_SKIPPED"
+  printf "  Failed:    %d\n" "$SUMMARY_FAILED"
+  echo
+  echo "Re-run: make audit"
+}
+
 # Category filter: CATEGORY=python,go or --category=python
 CATEGORY_FILTER="${CATEGORY:-}"
 for arg in "$@"; do
@@ -139,6 +165,17 @@ osc8() {
   [ -n "$url" ] && printf '\e]8;;%s\e\\%s\e]8;;\e\\' "$url" "$text" || printf '%s' "$text"
 }
 
+# Print installed status line (reusable for auto-update and interactive prompts)
+print_installed_status() {
+  local installed="$1"
+  local method="$2"
+  if [ -z "$installed" ]; then
+    printf "    installed: not installed\n"
+  else
+    printf "    installed: %s via %s\n" "$installed" "${method:-unknown}"
+  fi
+}
+
 # Check for multiple installations and print warning if found
 # Args: catalog_tool_name
 # Returns: 0 always (informational only)
@@ -241,6 +278,7 @@ process_tool() {
     printf "    installed: %s via %s\n" "$installed" "$method"
     printf "    target:    %s (same)\n" "$(osc8 "$url" "$latest")"
     check_multi_installs "$catalog_tool"
+    SUMMARY_SKIPPED=$((SUMMARY_SKIPPED + 1))
     printf "    up-to-date; skipping.\n"
     return 0
   fi
@@ -264,8 +302,14 @@ process_tool() {
   # BUT: multi-version tools always prompt (more significant operation)
   if [ "$auto_update" = "true" ] && [ -z "$is_multi_version" ]; then
     printf "\n==> %s %s [auto-update]\n" "$icon" "$display"
-    printf "    installed: %s via %s\n" "${installed:-<none>}" "${method:-unknown}"
-    printf "    target:    %s\n" "$(osc8 "$url" "${latest:-<unknown>}")"
+    print_installed_status "$installed" "$method"
+    # Show target; for self-managed tools (skip_upstream) show "self-managed" instead of <unknown>
+    local target_display="${latest:-<unknown>}"
+    local skip_upstream="$(catalog_get_property "$catalog_tool" skip_upstream)"
+    if [ "$target_display" = "<unknown>" ] && [ "$skip_upstream" = "true" ]; then
+      target_display="self-managed"
+    fi
+    printf "    target:    %s\n" "$(osc8 "$url" "$target_display")"
     check_multi_installs "$catalog_tool"
     printf "    auto-updating...\n"
 
@@ -278,37 +322,51 @@ process_tool() {
     fi
 
     # Execute the install with version-specific environment variables
+    local auto_update_success=0
     if [ "$catalog_tool" = "python" ] || [ -n "$is_multi_version" ] && [ "$catalog_tool" = "python" ]; then
-      UV_PYTHON_SPEC="$latest" "$ROOT"/scripts/$install_cmd || true
+      UV_PYTHON_SPEC="$latest" "$ROOT"/scripts/$install_cmd && auto_update_success=1 || true
     elif [ "$catalog_tool" = "ruby" ]; then
-      RUBY_VERSION="$latest" "$ROOT"/scripts/$install_cmd || true
+      RUBY_VERSION="$latest" "$ROOT"/scripts/$install_cmd && auto_update_success=1 || true
     elif [ "$catalog_tool" = "php" ] && [ -n "$version_cycle" ]; then
-      PHP_VERSION="$version_cycle" "$ROOT"/scripts/$install_cmd || true
+      PHP_VERSION="$version_cycle" "$ROOT"/scripts/$install_cmd && auto_update_success=1 || true
     elif [ "$catalog_tool" = "node" ] && [ -n "$version_cycle" ]; then
-      NODE_VERSION="$version_cycle" "$ROOT"/scripts/$install_cmd || true
+      NODE_VERSION="$version_cycle" "$ROOT"/scripts/$install_cmd && auto_update_success=1 || true
     elif [ "$catalog_tool" = "go" ] && [ -n "$version_cycle" ]; then
-      GO_VERSION="$version_cycle" "$ROOT"/scripts/$install_cmd || true
+      GO_VERSION="$version_cycle" "$ROOT"/scripts/$install_cmd && auto_update_success=1 || true
     else
-      "$ROOT"/scripts/$install_cmd || true
+      "$ROOT"/scripts/$install_cmd && auto_update_success=1 || true
     fi
 
     # Re-audit with fresh collection for this specific tool
     CLI_AUDIT_JSON=1 CLI_AUDIT_COLLECT=1 CLI_AUDIT_MERGE=1 "$CLI" audit.py "$tool" >/dev/null 2>&1 || true
     reload_audit_json
     # Clean up any already-current marker left by installer
     rm -f "/tmp/.cli-audit/${catalog_tool}.already-current"
+    if [ "$auto_update_success" = "0" ]; then
+      SUMMARY_FAILED=$((SUMMARY_FAILED + 1))
+    elif [ -z "$installed" ]; then
+      SUMMARY_INSTALLED=$((SUMMARY_INSTALLED + 1))
+    else
+      SUMMARY_UPDATED=$((SUMMARY_UPDATED + 1))
+    fi
     return 0
   fi
 
   # Prompt for installation/update
   printf "\n==> %s %s\n" "$icon" "$display"
   [ -n "$description" ] && printf "    %s\n" "$description"
   [ -n "$homepage" ] && printf "    Homepage: %s\n" "$(osc8 "$homepage" "$homepage")"
-  printf "    installed: %s via %s\n" "${installed:-<none>}" "${method:-unknown}"
+  print_installed_status "$installed" "$method"
 
   check_multi_installs "$catalog_tool"
 
-  printf "    target:    %s\n" "$(osc8 "$url" "${latest:-<unknown>}")"
+  # Show target; for self-managed tools (skip_upstream) show "self-managed" instead of <unknown>
+  local target_display_p="${latest:-<unknown>}"
+  local skip_upstream_p="$(catalog_get_property "$catalog_tool" skip_upstream)"
+  if [ "$target_display_p" = "<unknown>" ] && [ "$skip_upstream_p" = "true" ]; then
+    target_display_p="self-managed"
+  fi
+  printf "    target:    %s\n" "$(osc8 "$url" "$target_display_p")"
 
   # Build install command from catalog metadata (use catalog_tool for script name)
   local install_cmd="install_tool.sh $catalog_tool"
@@ -335,7 +393,7 @@ process_tool() {
     fi
     printf "      r = Remove/uninstall this tool\n"
     if [ -n "$is_multi_version" ]; then
-      printf "      P = Skip ALL %s cycles (never install any %s)\n" "$catalog_tool" "$catalog_tool"
+      printf "      P = Skip ALL outdated %s cycles\n" "$catalog_tool"
     fi
   else
     printf "      y = Install now\n"
@@ -344,7 +402,7 @@ process_tool() {
     printf "      s = Skip only %s (ask again when newer patch available)\n" "$latest"
     if [ -n "$is_multi_version" ]; then
       printf "      p = Never install %s (skip entire %s.x cycle)\n" "$display" "$version_cycle"
-      printf "      P = Skip ALL %s cycles (never install any %s)\n" "$catalog_tool" "$catalog_tool"
+      printf "      P = Skip ALL outdated %s cycles\n" "$catalog_tool"
     else
       printf "      p = Never install (permanently skip this tool)\n"
     fi
@@ -419,6 +477,7 @@ process_tool() {
       if [ "$upgrade_success" = "0" ]; then
         # Install script failed
         printf "\n    ⚠️  Upgrade failed (install script error)\n"
+        SUMMARY_FAILED=$((SUMMARY_FAILED + 1))
         prompt_pin_version "$tool" "$installed"
       elif [ -n "$binary_already_current" ]; then
         # Binary hash matches target release - upgrade succeeded despite version string
@@ -435,6 +494,7 @@ process_tool() {
         fi
       else
         # Upgrade succeeded - remove any existing pin to avoid stale pins
+        SUMMARY_UPDATED=$((SUMMARY_UPDATED + 1))
         local existing_pin="$(pins_get "$tool")"
         if [ -n "$existing_pin" ] && [ "$existing_pin" != "never" ]; then
           "$ROOT"/scripts/unpin_version.sh "$tool" || true
@@ -478,18 +538,23 @@ process_tool() {
       if [ "$upgrade_success_a" = "0" ]; then
         printf "\n    ⚠️  Upgrade failed (install script error)\n"
         printf "    Auto-update is still enabled - will try again next time.\n"
+        SUMMARY_FAILED=$((SUMMARY_FAILED + 1))
       elif [ -n "$binary_already_current_a" ]; then
         printf "    ✓ Auto-update enabled. Binary already matches target release.\n"
+        SUMMARY_UPDATED=$((SUMMARY_UPDATED + 1))
       elif [ "$new_installed_a" = "$installed" ] && [ "$new_installed_a" != "$latest" ]; then
         # Version didn't change - but check for prefix match (e.g., 3.13 vs 3.13.11)
         if [[ "$latest" == "$new_installed_a"* ]] || [[ "$new_installed_a" == "$latest"* ]]; then
           printf "    ✓ Auto-update enabled. This tool will update automatically in future.\n"
+          SUMMARY_UPDATED=$((SUMMARY_UPDATED + 1))
         else
           printf "\n    ⚠️  Upgrade did not succeed (version unchanged)\n"
           printf "    Auto-update is still enabled - will try again next time.\n"
+          SUMMARY_FAILED=$((SUMMARY_FAILED + 1))
         fi
       else
         printf "    ✓ Auto-update enabled. This tool will update automatically in future.\n"
+        SUMMARY_UPDATED=$((SUMMARY_UPDATED + 1))
         # Remove any existing pin
         local existing_pin_a="$(pins_get "$tool")"
         if [ -n "$existing_pin_a" ]; then
@@ -501,6 +566,7 @@ process_tool() {
       # Skip this specific patch version only
       printf "    Skipping only %s (will prompt again when newer patch available)\n" "$latest"
       "$ROOT"/scripts/pin_version.sh "$tool" "$latest" || true
+      SUMMARY_SKIPPED=$((SUMMARY_SKIPPED + 1))
       ;;
     [p])
       if [ -n "$installed" ]; then
@@ -550,8 +616,18 @@ process_tool() {
         local still_installed="$(json_field "$tool" installed)"
         if [ -z "$still_installed" ]; then
           printf "    ✓ %s has been removed\n" "$tool"
+          SUMMARY_REMOVED=$((SUMMARY_REMOVED + 1))
         else
-          printf "    ⚠️  %s may not have been fully removed (still detected: %s)\n" "$tool" "$still_installed"
+          # Check if remaining installation is a system/apt binary that we can't remove
+          local remaining_method="$(json_field "$tool" installed_method)"
+          if [ "$remaining_method" = "apt" ] || [ "$remaining_method" = "system" ]; then
+            printf "    ✓ User-managed %s removed (system %s still present at %s — managed by OS)\n" \
+              "$tool" "$still_installed" "$remaining_method"
+            SUMMARY_REMOVED=$((SUMMARY_REMOVED + 1))
+          else
+            printf "    ⚠️  %s may not have been fully removed (still detected: %s via %s)\n" "$tool" "$still_installed" "${remaining_method:-unknown}"
+            SUMMARY_FAILED=$((SUMMARY_FAILED + 1))
+          fi
         fi
       else
         printf "    Tool is not installed, nothing to remove\n"
@@ -570,6 +646,7 @@ process_tool() {
       ;;
     *)
       # User declined (N or empty)
+      SUMMARY_SKIPPED=$((SUMMARY_SKIPPED + 1))
       ;;
   esac
 }
@@ -863,7 +940,7 @@ for category in $(printf '%s\n' "${!CATEGORY_TOOLS[@]}" | while read c; do echo
   # Category-level prompt (skip if auto-yes mode)
   if [ "${AUTO_YES_ALL:-}" != "1" ]; then
     printf "  Tools: %s\n" "$(echo $tools | tr ' ' ', ' | sed 's/^, //')"
-    printf "  Process this category? [Y/n/a=all/s=skip-all] "
+    printf "  Process this category? [Y/n/a=all categories/s=skip-all] "
 
     cat_ans=""
     if [ -t 0 ]; then
@@ -935,5 +1012,6 @@ if [ -n "$DEPRECATED_TOOLS" ]; then
   fi
 fi
 
+# Print final summary
 echo
-echo "All done. Re-run: make audit"
+print_summary ""

scripts/install_node.sh

@@ -38,6 +38,8 @@ get_specific_node_version() {
 install_node() {
   ensure_nvm
   nvm install "$NODE_CHANNEL"
+  # Re-source nvm to ensure the new version is active in this shell
+  ensure_nvm_loaded
 
   # Only set default if this is NOT a multi-version install
   # (multi-version = specific major version like 24, 25)
@@ -66,6 +68,8 @@ install_node() {
 update_node() {
   ensure_nvm
   nvm install "$NODE_CHANNEL"
+  # Re-source nvm to ensure the new version is active in this shell
+  ensure_nvm_loaded
 
   # Only set default and update global packages if NOT a multi-version install
   if [ -z "${NODE_VERSION:-}" ]; then