Fix pre-existing issues and update README for v2.0

- Fix _infer_state_from_artifacts: SPEC-only maps to research (was bug_find)
- Fix cmd_validate_folder: corrupted .state files now error instead of silent fallback
- Fix upgrade.sh: remove || true, add python3 check, use git rev-parse --git-dir
- Update README.md with --project flag, --can-edit modes, --upgrade, enforcement layers
- Add 6 new tests for inference and validation fixes
- Complete hook-install-process and readme-upgrade-docs tasks

tasks/readme-upgrade-docs/SPEC.md

@@ -0,0 +1,23 @@
+# README and Upgrade Documentation Update
+
+## Goal
+Update README.md with complete, clear documentation for v2.0 features: `--project` flag, `--upgrade`, `--can-edit` project-level mode, pre-commit hook installation, and the full upgrade process for existing projects.
+
+## Requirements
+- Quick Reference includes `--project` on every command
+- `--can-edit` project-level modes documented with examples
+- `--upgrade` documented for untracked tasks
+- Enforcement layers section (pre-edit hook, pre-commit hook, prompt rules)
+- Upgrade process for existing projects (step-by-step for newcomers)
+- Pre-commit hook installation instructions in Project Setup and Upgrading sections
+- Key Components updated with new files
+
+## Acceptance Criteria
+- [x] All `status.py` examples include `--project`
+- [x] `--can-edit` modes documented
+- [x] `--upgrade` for untracked tasks documented
+- [x] Three enforcement layers documented
+- [x] Upgrade process for existing projects is step-by-step
+- [x] Pre-commit hook installation in both Project Setup and Upgrading
+- [x] Key Components updated
+- [x] 200 tests pass