Fix tools path resolution and add tests

- Use _resolve_repository_path() for explore, terminal and code commands
  so tools no longer rely on a 'directory' key in the repository dict.
- Fall back to repositories_base_dir/repositories_dir via get_repo_dir()
  when no explicit path-like key is present.
- Make VS Code workspace creation more robust (safe default for
  directories.workspaces and UTF-8 when writing JSON).
- Add unit tests for handle_tools_command (explore, terminal, code) under
  tests/unit/pkgmgr/cli/commands/test_tools.py.
- Add E2E/integration-style tests for the tools subcommands' --help
  output under tests/e2e/test_tools_help.py, treating SystemExit(0) as
  success.

This change fixes the KeyError: 'directory' when running 'pkgmgr code'
and verifies the behavior via unit and integration tests.

https://chatgpt.com/share/69393ca1-b554-800f-9967-abf8c4e3fea3

tests/e2e/test_tools_help.py

@@ -0,0 +1,74 @@
+"""
+E2E/Integration tests for the tool-related subcommands' --help output.
+
+We assert that calling:
+  - pkgmgr explore --help
+  - pkgmgr terminal --help
+  - pkgmgr code --help
+
+completes successfully. For --help, argparse exits with SystemExit(0),
+which we treat as success and suppress in the helper.
+"""
+
+from __future__ import annotations
+
+import os
+import runpy
+import sys
+import unittest
+from typing import List
+
+
+# Resolve project root (the repo where main.py lives, e.g. /src)
+PROJECT_ROOT = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "..", "..")
+)
+MAIN_PATH = os.path.join(PROJECT_ROOT, "main.py")
+
+
+def _run_main(argv: List[str]) -> None:
+    """
+    Helper to run main.py with the given argv.
+
+    This mimics a "pkgmgr ..." invocation in the E2E container.
+
+    For --help invocations, argparse will call sys.exit(0), which raises
+    SystemExit(0). We treat this as success and only re-raise non-zero
+    exit codes.
+    """
+    old_argv = sys.argv
+    try:
+        sys.argv = ["pkgmgr"] + argv
+        try:
+            runpy.run_path(MAIN_PATH, run_name="__main__")
+        except SystemExit as exc:  # argparse uses this for --help
+            # SystemExit.code can be int, str or None; for our purposes:
+            code = exc.code
+            if code not in (0, None):
+                # Non-zero exit code -> real error.
+                raise
+            # For 0/None: treat as success and swallow the exception.
+    finally:
+        sys.argv = old_argv
+
+
+class TestToolsHelp(unittest.TestCase):
+    """
+    E2E/Integration tests for tool commands' --help screens.
+    """
+
+    def test_explore_help(self) -> None:
+        """Ensure `pkgmgr explore --help` runs successfully."""
+        _run_main(["explore", "--help"])
+
+    def test_terminal_help(self) -> None:
+        """Ensure `pkgmgr terminal --help` runs successfully."""
+        _run_main(["terminal", "--help"])
+
+    def test_code_help(self) -> None:
+        """Ensure `pkgmgr code --help` runs successfully."""
+        _run_main(["code", "--help"])
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/unit/pkgmgr/cli/commands/test_tools.py

@@ -0,0 +1,168 @@
+from __future__ import annotations
+
+import json
+import os
+import tempfile
+import unittest
+from types import SimpleNamespace
+from typing import Any, Dict, List
+
+from pkgmgr.cli.commands.tools import handle_tools_command
+
+Repository = Dict[str, Any]
+
+
+class _Args:
+    """
+    Simple helper object to mimic argparse.Namespace for handle_tools_command.
+    """
+
+    def __init__(self, command: str) -> None:
+        self.command = command
+
+
+class TestHandleToolsCommand(unittest.TestCase):
+    """
+    Unit tests for pkgmgr.cli.commands.tools.handle_tools_command.
+
+    We focus on:
+      - Correct path resolution for repositories that have a 'directory' key.
+      - Correct shell commands for 'explore' and 'terminal'.
+      - Proper workspace creation and invocation of 'code' for the 'code' command.
+    """
+
+    def setUp(self) -> None:
+        # Two fake repositories with explicit 'directory' entries so that
+        # _resolve_repository_path() does not need to call get_repo_dir().
+        self.repos: List[Repository] = [
+            {"alias": "repo1", "directory": "/tmp/repo1"},
+            {"alias": "repo2", "directory": "/tmp/repo2"},
+        ]
+
+        # Minimal CLI context; only attributes used in tools.py are provided.
+        self.ctx = SimpleNamespace(
+            config_merged={"directories": {"workspaces": "~/Workspaces"}},
+            all_repositories=self.repos,
+            repositories_base_dir="/base/dir",
+        )
+
+    # ------------------------------------------------------------------ #
+    # Helper
+    # ------------------------------------------------------------------ #
+
+    def _patch_run_command(self):
+        """
+        Convenience context manager for patching run_command in tools module.
+        """
+        from unittest.mock import patch
+
+        return patch("pkgmgr.cli.commands.tools.run_command")
+
+    # ------------------------------------------------------------------ #
+    # Tests for 'explore'
+    # ------------------------------------------------------------------ #
+
+    def test_explore_uses_directory_paths(self) -> None:
+        """
+        The 'explore' command should call Nautilus with the resolved
+        repository paths and use '& disown' as in the implementation.
+        """
+        from unittest.mock import call
+
+        args = _Args(command="explore")
+
+        with self._patch_run_command() as mock_run_command:
+            handle_tools_command(args, self.ctx, self.repos)
+
+        expected_calls = [
+            call('nautilus "/tmp/repo1" & disown'),
+            call('nautilus "/tmp/repo2" & disown'),
+        ]
+        self.assertEqual(mock_run_command.call_args_list, expected_calls)
+
+    # ------------------------------------------------------------------ #
+    # Tests for 'terminal'
+    # ------------------------------------------------------------------ #
+
+    def test_terminal_uses_directory_paths(self) -> None:
+        """
+        The 'terminal' command should open a GNOME Terminal tab with the
+        repository as its working directory.
+        """
+        from unittest.mock import call
+
+        args = _Args(command="terminal")
+
+        with self._patch_run_command() as mock_run_command:
+            handle_tools_command(args, self.ctx, self.repos)
+
+        expected_calls = [
+            call('gnome-terminal --tab --working-directory="/tmp/repo1"'),
+            call('gnome-terminal --tab --working-directory="/tmp/repo2"'),
+        ]
+        self.assertEqual(mock_run_command.call_args_list, expected_calls)
+
+    # ------------------------------------------------------------------ #
+    # Tests for 'code'
+    # ------------------------------------------------------------------ #
+
+    def test_code_creates_workspace_and_calls_code(self) -> None:
+        """
+        The 'code' command should:
+
+          - Build a workspace file name from sorted repository identifiers.
+          - Resolve the repository paths into VS Code 'folders'.
+          - Create the workspace file if it does not exist.
+          - Call 'code "<workspace_file>"' via run_command.
+        """
+        from unittest.mock import patch
+
+        args = _Args(command="code")
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Patch expanduser so that the configured '~/Workspaces'
+            # resolves into our temporary directory.
+            with patch(
+                "pkgmgr.cli.commands.tools.os.path.expanduser"
+            ) as mock_expanduser:
+                mock_expanduser.return_value = tmpdir
+
+                # Patch get_repo_identifier so the resulting workspace file
+                # name is deterministic and easy to assert.
+                with patch(
+                    "pkgmgr.cli.commands.tools.get_repo_identifier"
+                ) as mock_get_identifier:
+                    mock_get_identifier.side_effect = ["repo-b", "repo-a"]
+
+                    with self._patch_run_command() as mock_run_command:
+                        handle_tools_command(args, self.ctx, self.repos)
+
+                    # The identifiers are ['repo-b', 'repo-a'], which are
+                    # sorted to ['repo-a', 'repo-b'] and joined with '_'.
+                    expected_workspace_name = "repo-a_repo-b.code-workspace"
+                    expected_workspace_file = os.path.join(
+                        tmpdir, expected_workspace_name
+                    )
+
+                    # Workspace file should have been created.
+                    self.assertTrue(
+                        os.path.exists(expected_workspace_file),
+                        "Workspace file was not created.",
+                    )
+
+                    # The content of the workspace must be valid JSON with
+                    # the expected folder paths.
+                    with open(expected_workspace_file, "r", encoding="utf-8") as f:
+                        data = json.load(f)
+
+                    self.assertIn("folders", data)
+                    folder_paths = {f["path"] for f in data["folders"]}
+                    self.assertEqual(
+                        folder_paths,
+                        {"/tmp/repo1", "/tmp/repo2"},
+                    )
+
+                    # And VS Code must have been invoked with that workspace.
+                    mock_run_command.assert_called_once_with(
+                        f'code "{expected_workspace_file}"'
+                    )