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/pre-existing-fixes/ADVERSARIAL_BUG_REPORT.md

@@ -0,0 +1,14 @@
+# Adversarial Bug Report: Pre-existing Fixes
+
+## Deep Bugs Found: 0
+
+No code paths introduced regressions. Verified:
+- `_infer_state_from_artifacts` logic trace correct for all artifact combinations
+- `cmd_validate_folder` now properly catches corrupted `.state` files
+- `upgrade.sh` will now fail visibly instead of silently succeeding
+- `git rev-parse --git-dir` works for worktrees (returns `.git/worktrees/<name>`)
+- Edge case: bare repos (`--git-dir` returns the repo path itself) — hooks directory is `<repo>/hooks/` which `mkdir -p` handles correctly
+
+## Pre-existing Issues Still Not In Scope
+- Lock timeout parsing in multi-agent mode is case-sensitive
+- Audit Category 3 (git modification check) is stubbed