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/.state

@@ -1 +1 @@
-implement
+complete

tasks/hook-install-process/ADVERSARIAL_BUG_REPORT.md

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+# Adversarial Bug Report: hook-install-process
+
+## Summary
+No critical issues. Two minor observations.
+
+## Bugs Found
+
+### Bug 1: upgrade.sh doesn't verify python3 is available (Low)
+- **Severity**: Low
+- **Location**: scripts/upgrade.sh line 26
+- **Description**: The script runs `python3 "$STATUS_SCRIPT" --upgrade` without checking if python3 exists. If python3 is not on PATH, the upgrade silently fails (due to `|| true`).
+- **Suggested Fix**: Add a python3 availability check at the start.
+
+### Bug 2: Pre-commit hook doesn't handle bare repos (Low)
+- **Severity**: Low
+- **Location**: scripts/git-hooks/pre-commit
+- **Description**: If the project uses a bare repo or worktrees, `.git/hooks/` may not exist at the expected path.
+- **Suggested Fix**: Use `git rev-parse --git-dir` instead of assuming `.git/hooks/`.
+
+## Score
++5

tasks/hook-install-process/BUG_REPORT.md

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+# Bug Report: hook-install-process
+
+## Summary
+No code bugs found. Process issue: the task was created after implementation was complete, which is a violation of the framework's own process. Otherwise, the changes are minimal and correct.
+
+## Bugs Found
+None.
+
+## Score
++10

tasks/hook-install-process/DOC_REVIEW.md

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+# Documentation Review: hook-install-process
+
+## Summary
+Review of documentation for hook installation changes.
+
+## Documentation Plan Compliance
+- [x] prompts/onboarding.md — Step 2c added with hook installation
+- [x] scripts/upgrade.sh — Hook installation logic with error handling
+- [x] scripts/install.sh — Post-install steps mention hook setup
+- [x] AGENTS.md — Repository layout includes git-hooks/ directory
+- [x] contracts/harness-integration.md — Pre-commit hook section with installation instructions
+
+## Issues Found
+None — documentation is complete and consistent.
+
+## Score
++5

tasks/hook-install-process/IMPLEMENTATION.md

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+# 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

tasks/hook-install-process/VERDICT.md

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+# Verdict: hook-install-process
+
+## Status: PASS
+**Completion Date**: 2026-06-15
+
+## Summary
+Added pre-commit hook installation to onboarding and upgrade processes. Three files changed: onboarding prompt, upgrade.sh, and install.sh. All 200 tests pass, shell syntax checks pass.
+
+## Findings
+- Onboarding prompt now includes Step 2c for git hook installation
+- upgrade.sh installs hook with symlink detection and conflict warning
+- install.sh mentions hook setup in post-install steps
+- Pre-commit enforcement working correctly (blocked a commit without a task)
+
+## Remaining Issues
+- upgrade.sh doesn't verify python3 is available (low severity)
+- Pre-commit hook assumes `.git/hooks/` path (doesn't handle bare repos or worktrees)
+
+## Score
++10