feat: enhance workflow and testing infrastructure

- Introduced ExecutionMode type for project execution modes (parallel, sequential).
- Updated SetupOpts to use ExecutionMode instead of string literals.
- Enhanced workflow states to include a new "In Review" state with appropriate transitions.
- Implemented TestHarness for end-to-end testing, including command interception and workspace setup.
- Created TestProvider for in-memory issue tracking during tests.
- Refactored project registration and setup tools to utilize ExecutionMode.
- Updated various tools to ensure compatibility with new workflow and execution modes.
- Added new dependencies: cockatiel for resilience and zod for schema validation.

package.json

@@ -55,6 +55,8 @@
     "typescript": "^5.9.3"
   },
   "dependencies": {
-    "yaml": "^2.8.2"
+    "cockatiel": "^3.2.1",
+    "yaml": "^2.8.2",
+    "zod": "^4.3.6"
   }
 }