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/hook-install-process/IMPLEMENTATION.md

@@ -0,0 +1,27 @@
+# Implementation: Hook Installation in Onboarding and Upgrade
+
+## Changes
+
+### 1. prompts/onboarding.md — Step 2c: Pre-Commit Hook Installation
+- Added Step 2c between VRAM config and Output sections
+- Checks for `.git/hooks/` directory
+- Creates symlink from `.git/hooks/pre-commit` to `~/.automaton/scripts/git-hooks/pre-commit`
+- Warns if existing hook is not our symlink
+- Verifies hook works with `status.py --can-edit`
+
+### 2. scripts/upgrade.sh — Hook installation during upgrade
+- Added after the "Upgrade Complete" message
+- Detects `.git/hooks/` directory
+- If hook doesn't exist: creates symlink
+- If hook is already our symlink: reports "already linked"
+- If hook exists but is not our symlink: warns user, prints manual install command
+- If no `.git/hooks/`: prints note with manual install command
+
+### 3. scripts/install.sh — Post-install next steps
+- Replaced single "Next step" with numbered list
+- Added hook installation as step 2
+- Added explanation of what the hook does
+
+## Tests
+- All 200 tests pass
+- Shell syntax checks pass for install.sh and upgrade.sh