fix: preserve uninstalled optional package managers

scripts/install_node.sh

@@ -81,6 +81,14 @@
 }
 
 update_node() {
+  # Preserve deliberate uninstalls across the Node.js version switch. nvm
+  # installs a fresh prefix, so checking after the switch would lose whether
+  # these optional package managers existed beforehand.
+  local had_pnpm=0
+  local had_yarn=0
+  command -v pnpm >/dev/null 2>&1 && had_pnpm=1
+  command -v yarn >/dev/null 2>&1 && had_yarn=1
+
   ensure_nvm
   nvm install "$NODE_CHANNEL"
   # Re-source nvm to ensure the new version is active in this shell
@@ -98,12 +106,17 @@
       nvm alias default "$NODE_CHANNEL" || true
       nvm use default || true
     fi
-    # Ensure corepack shims are present
-    corepack enable 2>/dev/null || true
     npm install -g npm@latest || true
-    # Update pnpm and yarn via corepack; fall back to npm global if corepack unavailable
-    corepack prepare pnpm@latest --activate 2>/dev/null || npm install -g pnpm@latest || true
-    corepack prepare yarn@1 --activate 2>/dev/null || npm install -g yarn@latest || true
+    # Only restore/update package managers that were installed before the
+    # Node.js update. Explicit installs still enable both in install_node().
+    if [ "$had_pnpm" -eq 1 ]; then
+      corepack enable pnpm 2>/dev/null || true
+      corepack prepare pnpm@latest --activate 2>/dev/null || npm install -g pnpm@latest || true
+    fi
+    if [ "$had_yarn" -eq 1 ]; then
+      corepack enable yarn 2>/dev/null || true
+      corepack prepare yarn@1 --activate 2>/dev/null || npm install -g yarn@latest || true
+    fi
     npm update -g eslint prettier || true
   else
     echo "=> Node.js version $NODE_VERSION has been updated"
@@ -168,7 +181,8 @@
     after="$(get_specific_node_version "$NODE_CHANNEL")"
     # Get path to the specific version's node binary
     local nvm_dir="${NVM_DIR:-$HOME/.nvm}"
-    local resolved_ver="$(nvm version "$NODE_CHANNEL" 2>/dev/null || true)"
+    local resolved_ver
+    resolved_ver="$(nvm version "$NODE_CHANNEL" 2>/dev/null || true)"
     if [ -n "$resolved_ver" ] && [ "$resolved_ver" != "N/A" ]; then
       path="$nvm_dir/versions/node/$resolved_ver/bin/node"
     fi
@@ -191,5 +205,3 @@
   reconcile) reconcile_node ;;
   *) echo "Usage: $0 {install|update|uninstall|reconcile}" ; exit 2 ;;
 esac
-
-

scripts/install_python.sh

@@ -127,7 +127,10 @@ install_or_update_py_cli() {
       if [ "$cmd" = install ]; then
         uv tool install -q "$p" >/dev/null 2>&1 || true
       else
-        uv tool upgrade -q "$p" >/dev/null 2>&1 || uv tool install -q "$p" >/dev/null 2>&1 || true
+        # Upgrade only tools that are already installed. A failed upgrade
+        # commonly means that the tool was deliberately removed; installing it
+        # here would undo `make uninstall-<tool>`.
+        uv tool upgrade -q "$p" >/dev/null 2>&1 || true
       fi
     done
   else
@@ -139,7 +142,7 @@ install_or_update_py_cli() {
       if [ "$cmd" = install ]; then
         pipx install "$p" >/dev/null 2>&1 || true
       else
-        pipx upgrade "$p" >/dev/null 2>&1 || pipx install "$p" >/dev/null 2>&1 || true
+        pipx upgrade "$p" >/dev/null 2>&1 || true
       fi
     done
   fi
@@ -270,5 +273,3 @@ case "$ACTION" in
   reconcile) reconcile_py_tools ;;
   *) echo "Usage: $0 {install|update|uninstall|reconcile}" ; exit 2 ;;
 esac
-
-

scripts/install_tool.sh

@@ -7,6 +7,8 @@ DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 # Source reconciliation libraries
 . "$DIR/lib/reconcile.sh"
+# Source snapshot refresh helper used after uninstall.
+. "$DIR/lib/install_strategy.sh"
 # Source bash-completion lifecycle helpers (install_completion / remove_completion /
 # post_install_completion). All completion operations are best-effort.
 . "$DIR/lib/completion.sh"
@@ -60,6 +62,7 @@ if [ "$ACTION" = "uninstall" ]; then
     if [ -n "$script_name" ] && [ -f "$DIR/$script_name" ]; then
       "$DIR/$script_name" uninstall || true
     fi
+    refresh_snapshot "$TOOL" || true
     # Dedicated scripts handle their own cleanup completely
     # Don't try to detect and remove additional installations
     # (especially important for multi-version tools like node, python, go)
@@ -75,6 +78,7 @@ if [ "$ACTION" = "uninstall" ]; then
 
   if [ "$install_count" -eq 0 ]; then
     echo "[$TOOL] Successfully removed"
+    refresh_snapshot "$TOOL" || true
     exit 0
   fi
 
@@ -113,6 +117,7 @@ if [ "$ACTION" = "uninstall" ]; then
       echo "  • $method: $path"
     done
   fi
+  refresh_snapshot "$TOOL" || true
   exit 0
 fi
 

scripts/install_yarn.sh

@@ -3,8 +3,9 @@
 
 DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 . "$DIR/lib/common.sh"
+. "$DIR/lib/install_strategy.sh"
 
-ACTION="${1:-update}"
+ACTION="${1:-install}"
 
 check_nvm_node() {
   # Check if Node.js is nvm-managed (resolve symlinks)
@@ -27,6 +28,7 @@
 }
 
 update_yarn() {
+  local allow_install="${1:-false}"
   ensure_nvm_loaded
 
   if ! command -v node >/dev/null 2>&1; then
@@ -44,13 +46,18 @@
     return 1
   fi
 
+  if ! command -v yarn >/dev/null 2>&1 && [ "$allow_install" != "true" ]; then
+    echo "[yarn] Yarn is not installed; skipping update" >&2
+    return 0
+  fi
+
   local before after path
   before="$(yarn --version 2>/dev/null || echo '<none>')"
 
   # Try corepack first (modern approach)
   if command -v corepack >/dev/null 2>&1; then
     echo "[yarn] Updating yarn via corepack..." >&2
-    corepack enable || true
+    corepack enable yarn || true
     corepack prepare yarn@stable --activate || true
   else
     # Fallback to npm global install
@@ -69,7 +76,7 @@
 install_yarn() {
   echo "[yarn] yarn should be installed via Node.js corepack/npm. Installing/updating Node.js first..."
   "$DIR/install_node.sh" install || true
-  update_yarn
+  update_yarn true
 }
 
 reconcile_yarn() {
@@ -89,13 +96,26 @@
     apt_remove_if_present cmdtest yarnpkg || true
   fi
 
-  update_yarn
+  update_yarn true
 }
 
 uninstall_yarn() {
-  echo "[yarn] yarn is managed by Node.js/npm. To remove:" >&2
-  echo "[yarn]   npm uninstall -g yarn" >&2
-  echo "[yarn]   or: corepack disable" >&2
+  ensure_nvm_loaded
+
+  if command -v npm >/dev/null 2>&1; then
+    npm uninstall -g yarn >/dev/null 2>&1 || true
+  fi
+  if command -v corepack >/dev/null 2>&1; then
+    corepack disable yarn >/dev/null 2>&1 || true
+  fi
+
+  refresh_snapshot "yarn" || true
+
+  if command -v yarn >/dev/null 2>&1; then
+    echo "[yarn] Warning: Yarn is still available at $(command -v yarn)" >&2
+    return 1
+  fi
+  echo "[yarn] Successfully removed"
 }
 
 case "$ACTION" in

tests/test_preserve_optional_tools.py

@@ -0,0 +1,138 @@
+"""Regression tests for preserving deliberately uninstalled optional tools."""
+
+import os
+import subprocess
+import tempfile
+from pathlib import Path
+
+import pytest
+
+PROJECT_ROOT = Path(__file__).parent.parent
+PYTHON_INSTALLER = PROJECT_ROOT / "scripts" / "install_python.sh"
+NODE_INSTALLER = PROJECT_ROOT / "scripts" / "install_node.sh"
+TOOL_INSTALLER = PROJECT_ROOT / "scripts" / "install_tool.sh"
+YARN_INSTALLER = PROJECT_ROOT / "scripts" / "install_yarn.sh"
+POSIX_SHELL_ONLY = pytest.mark.skipif(os.name == "nt", reason="Behavioral shell tests require a POSIX host")
+
+
+def _write_stub(directory: Path, name: str, body: str) -> Path:
+    stub = directory / name
+    stub.write_text(f"#!/usr/bin/env bash\n{body}\n")
+    stub.chmod(0o755)
+    return stub
+
+
+def test_python_upgrade_does_not_fall_back_to_install():
+    """A missing uv/pipx tool must stay missing during a stack update."""
+    content = PYTHON_INSTALLER.read_text()
+
+    assert 'uv tool upgrade -q "$p" >/dev/null 2>&1 || uv tool install' not in content
+    assert 'pipx upgrade "$p" >/dev/null 2>&1 || pipx install' not in content
+
+
+def test_python_explicit_install_still_installs_cli_tools():
+    """The explicit install operation must retain its existing semantics."""
+    content = PYTHON_INSTALLER.read_text()
+
+    assert 'uv tool install -q "$p"' in content
+    assert 'pipx install "$p"' in content
+
+
+def test_node_update_records_optional_package_managers_before_switching_node():
+    """Node updates must remember which optional managers existed beforehand."""
+    content = NODE_INSTALLER.read_text()
+    update_body = content.split("update_node() {", 1)[1].split("\nuninstall_node() {", 1)[0]
+
+    ensure_nvm_position = update_body.index("ensure_nvm")
+    assert update_body.index("command -v pnpm") < ensure_nvm_position
+    assert update_body.index("command -v yarn") < ensure_nvm_position
+
+
+def test_node_update_only_prepares_previously_installed_package_managers():
+    """Corepack/npm must not bring yarn or pnpm back after uninstall."""
+    content = NODE_INSTALLER.read_text()
+    update_body = content.split("update_node() {", 1)[1].split("\nuninstall_node() {", 1)[0]
+
+    assert 'if [ "$had_pnpm" -eq 1 ]; then' in update_body
+    assert 'if [ "$had_yarn" -eq 1 ]; then' in update_body
+    assert "corepack enable 2>" not in update_body
+    assert "corepack enable pnpm" in update_body
+    assert "corepack enable yarn" in update_body
+    assert update_body.index('if [ "$had_pnpm" -eq 1 ]; then') < update_body.index("corepack prepare pnpm@latest")
+    assert update_body.index('if [ "$had_yarn" -eq 1 ]; then') < update_body.index("corepack prepare yarn@1")
+
+
+def test_generic_uninstall_refreshes_the_tool_snapshot():
+    """Recommendations must not use stale state after an uninstall."""
+    content = TOOL_INSTALLER.read_text()
+    uninstall_body = content.split('if [ "$ACTION" = "uninstall" ]; then', 1)[1].split(
+        "\n# Check if tool uses reconciliation system", 1
+    )[0]
+
+    assert '. "$DIR/lib/install_strategy.sh"' in content
+    assert uninstall_body.count('refresh_snapshot "$TOOL"') >= 2
+
+
+@POSIX_SHELL_ONLY
+def test_direct_yarn_update_keeps_missing_yarn_uninstalled():
+    """The dedicated `make upgrade-yarn` route must not bootstrap Yarn."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        temp = Path(tmpdir)
+        home = temp / "home"
+        nvm_bin = home / ".nvm" / "versions" / "node" / "v26.5.0" / "bin"
+        nvm_bin.mkdir(parents=True)
+        calls = temp / "calls.log"
+        _write_stub(nvm_bin, "node", "echo v26.5.0")
+        _write_stub(
+            nvm_bin,
+            "readlink",
+            'echo "$HOME/.nvm/versions/node/v26.5.0/bin/node"',
+        )
+        _write_stub(nvm_bin, "corepack", f'echo "corepack $*" >> "{calls}"')
+        _write_stub(nvm_bin, "npm", f'echo "npm $*" >> "{calls}"')
+
+        env = os.environ.copy()
+        env["HOME"] = str(home)
+        env["PATH"] = f"{nvm_bin}:/usr/bin:/bin"
+        result = subprocess.run(
+            ["bash", str(YARN_INSTALLER), "update"],
+            capture_output=True,
+            text=True,
+            env=env,
+            timeout=10,
+        )
+
+        assert result.returncode == 0, result.stderr
+        assert not calls.exists() or calls.read_text() == ""
+        assert "not installed" in (result.stdout + result.stderr).lower()
+
+
+@POSIX_SHELL_ONLY
+def test_direct_yarn_uninstall_removes_shims_and_refreshes_snapshot():
+    """The dedicated `make uninstall-yarn` route must do real cleanup."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        temp = Path(tmpdir)
+        home = temp / "home"
+        stub_bin = temp / "bin"
+        stub_bin.mkdir(parents=True)
+        calls = temp / "calls.log"
+        _write_stub(stub_bin, "npm", f'echo "npm $*" >> "{calls}"')
+        _write_stub(stub_bin, "corepack", f'echo "corepack $*" >> "{calls}"')
+        _write_stub(stub_bin, "python3", f'echo "python3 $*" >> "{calls}"')
+
+        env = os.environ.copy()
+        env["HOME"] = str(home)
+        env["PATH"] = f"{stub_bin}:/usr/bin:/bin"
+        result = subprocess.run(
+            ["bash", str(YARN_INSTALLER), "uninstall"],
+            capture_output=True,
+            text=True,
+            env=env,
+            timeout=10,
+        )
+
+        assert result.returncode == 0, result.stderr
+        log = calls.read_text()
+        assert "npm uninstall -g yarn" in log
+        assert "corepack disable yarn" in log
+        assert "audit.py yarn" in log