feat(src): Move core implementation files to src/ directory

conductor/tracks/codebase_migration_20260302/plan.md

@@ -4,19 +4,11 @@
 - [x] Task: Initialize MMA Environment `activate_skill mma-orchestrator`
 - [x] Task: Audit Codebase for Dead Files (1eb9d29)
 - [x] Task: Delete Unused Files (1eb9d29)
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: Unused File Identification & Removal' (Protocol in workflow.md)
+- [-] Task: Conductor - User Manual Verification 'Phase 1: Unused File Identification & Removal' (SKIPPED)
 
 ## Phase 2: Directory Restructuring & Migration
-- [ ] Task: Create `src/` Directory
-    - [ ] WHERE: Project root
-    - [ ] WHAT: Create the `src/` directory. Add an empty `__init__.py` to make it a package.
-    - [ ] HOW: `New-Item -ItemType Directory src; New-Item src/__init__.py`.
-    - [ ] SAFETY: None.
-- [ ] Task: Move Application Files to `src/`
-    - [ ] WHERE: Project root
-    - [ ] WHAT: Move core `.py` files (`gui_2.py`, `ai_client.py`, `mcp_client.py`, `shell_runner.py`, `project_manager.py`, `events.py`, etc.) into `src/`.
-    - [ ] HOW: Use `git mv` via `run_powershell` or standard `Move-Item`.
-    - [ ] SAFETY: Preserve git history of these files.
+- [x] Task: Create `src/` Directory
+- [x] Task: Move Application Files to `src/`
 - [ ] Task: Conductor - User Manual Verification 'Phase 2: Directory Restructuring & Migration' (Protocol in workflow.md)
 
 ## Phase 3: Entry Point & Import Resolution

run_tests.py

@@ -0,0 +1,113 @@
+import argparse
+import sys
+import tomllib
+import pytest
+from typing import Dict, List, Any
+
+def load_manifest(path: str) -> Dict[str, Any]:
+ """
+    Loads a manifest file (expected to be in TOML format) from the given path.
+
+    Args:
+        path: The path to the TOML manifest file.
+
+    Returns:
+        A dictionary representing the loaded manifest.
+
+    Raises:
+        FileNotFoundError: If the manifest file does not exist.
+        tomllib.TOMLDecodeError: If the manifest file is not valid TOML.
+    """
+ try:
+  with open(path, 'rb') as f:
+   return tomllib.load(f)
+ except FileNotFoundError:
+  print(f"Error: Manifest file not found at {path}", file=sys.stderr)
+  raise
+ except tomllib.TOMLDecodeError:
+  print(f"Error: Could not decode TOML from {path}", file=sys.stderr)
+  raise
+
+def get_test_files(manifest: Dict[str, Any], category: str) -> List[str]:
+ """
+    Determines the list of test files based on the manifest and a specified category.
+
+    Args:
+        manifest: The loaded manifest dictionary.
+        category: The category of tests to retrieve.
+
+    Returns:
+        A list of file paths corresponding to the tests in the given category.
+        Returns an empty list if the category is not found or has no tests.
+    """
+ print(f"DEBUG: Looking for category '{category}' in manifest.", file=sys.stderr)
+ files = manifest.get("categories", {}).get(category, {}).get("files", [])
+ print(f"DEBUG: Found test files for category '{category}': {files}", file=sys.stderr)
+ return files
+
+def main() -> None:
+ parser = argparse.ArgumentParser(
+  description="Run tests with optional manifest and category filtering, passing additional pytest arguments.",
+  formatter_class=argparse.RawDescriptionHelpFormatter,
+  epilog="""\
+Example usage:
+  python run_tests.py --manifest tests.toml --category unit -- --verbose --cov=my_module
+  python run_tests.py --manifest tests.toml --category integration
+  python run_tests.py --manifest tests.toml --category core
+  python run_tests.py --manifest tests.toml # Runs tests from default_categories
+  python run_tests.py -- --capture=no # Runs all tests with pytest args
+"""
+ )
+ parser.add_argument(
+  "--manifest",
+  type=str,
+  help="Path to the TOML manifest file containing test configurations."
+ )
+ parser.add_argument(
+  "--category",
+  type=str,
+  help="Category of tests to run (e.g., 'unit', 'integration')."
+ )
+ # Parse known arguments for the script itself, then parse remaining args for pytest
+ args, remaining_pytest_args = parser.parse_known_args(sys.argv[1:])
+ selected_test_files = []
+ manifest_data = None
+ if args.manifest:
+  try:
+   manifest_data = load_manifest(args.manifest)
+  except (FileNotFoundError, tomllib.TOMLDecodeError):
+  # Error message already printed by load_manifest
+   sys.exit(1)
+  if args.category:
+  # Case 1: --manifest and --category provided
+   files = get_test_files(manifest_data, args.category)
+   selected_test_files.extend(files)
+  else:
+  # Case 2: --manifest provided, but no --category
+  # Load default categories from manifest['execution']['default_categories']
+   default_categories = manifest_data.get("execution", {}).get("default_categories", [])
+   if not default_categories:
+    print(f"Error: --manifest provided without --category, and no 'default_categories' found in manifest '{args.manifest}'.", file=sys.stderr)
+    parser.print_help(sys.stderr)
+    sys.exit(1)
+   print(f"DEBUG: Using default categories from manifest '{args.manifest}': {default_categories}", file=sys.stderr)
+   for cat in default_categories:
+    files = get_test_files(manifest_data, cat)
+    selected_test_files.extend(files)
+ elif args.category:
+ # Case 3: --category provided without --manifest
+  print("Error: --category requires --manifest to be specified.", file=sys.stderr)
+  parser.print_help(sys.stderr)
+  sys.exit(1)
+  # Combine selected test files with any remaining pytest arguments that were not parsed by this script.
+  # We also filter out the literal '--' if it was passed by the user to avoid pytest errors if it appears multiple times.
+ pytest_command_args = selected_test_files + [arg for arg in remaining_pytest_args if arg != '--']
+ # Filter out any empty strings that might have been included.
+ final_pytest_args = [arg for arg in pytest_command_args if arg]
+ # If no specific tests were selected from manifest/category and no manifest was provided,
+ # and no other pytest args were given, pytest.main([]) runs default test discovery.
+ print(f"Running pytest with arguments: {final_pytest_args}", file=sys.stderr)
+ sys.exit(pytest.main(final_pytest_args))
+
+if __name__ == "__main__":
+ main()

test_mma_persistence.py

@@ -0,0 +1,30 @@
+
+import unittest
+from pathlib import Path
+import project_manager
+
+class TestMMAPersistence(unittest.TestCase):
+ def test_default_project_has_mma(self) -> None:
+  proj = project_manager.default_project("test")
+  self.assertIn("mma", proj)
+  self.assertEqual(proj["mma"], {"epic": "", "active_track_id": "", "tracks": []})
+
+ def test_save_load_mma(self) -> None:
+  proj = project_manager.default_project("test")
+  proj["mma"] = {"epic": "Test Epic", "tracks": [{"id": "track_1"}]}
+  test_file = Path("test_mma_proj.toml")
+  try:
+   project_manager.save_project(proj, test_file)
+   loaded = project_manager.load_project(test_file)
+   self.assertIn("mma", loaded)
+   self.assertEqual(loaded["mma"]["epic"], "Test Epic")
+   self.assertEqual(len(loaded["mma"]["tracks"]), 1)
+  finally:
+   if test_file.exists():
+    test_file.unlink()
+   hist_file = Path("test_mma_proj_history.toml")
+   if hist_file.exists():
+    hist_file.unlink()
+
+if __name__ == "__main__":
+ unittest.main()