name: update-brain description: Synchronize all brain/ files with current project state. Updates indexes, marks completed tasks, and logs changes. Run after every task completion.

Update Brain

Synchronize brain/ knowledge base with current project state.

Execution Protocol

Step 1: Scan Project Changes

Identify what changed since last update:

• New files created
• Sections added to pages
• Assets added
• Configuration changes

Step 2: Update general_index.md

If project structure changed (new folders/files):

## Recent Changes

| Date | Change | Location |
|------|--------|----------|
| [today] | Added [description] | `path/to/file` |

Step 3: Update codebase_index.md

For content changes, update the relevant page entry:

### `about.qmd` — CV/Resume Page

**Current State:**
- ✓ YAML front matter + intro
- ✓ Education section
- ✓ Professional Experience section
- ○ Technical Skills section (pending)
- ○ Research Interests section (pending)

**Status:** `In progress`

Track section-level progress, not just page-level.

Step 4: Update plan.md

Mark completed tasks:

### Task 2: Add Education section
- **Status:** ~~Pending~~ Complete ✓
- **Completed:** [timestamp]

Step 5: Verify Consistency

• All new files in general_index.md
• Section progress updated in codebase_index.md
• Completed tasks marked in plan.md

Output Format

═══════════════════════════════════════════════════════
  🧠 BRAIN UPDATE COMPLETE
═══════════════════════════════════════════════════════

✓ general_index.md    [no changes]
✓ codebase_index.md   [about.qmd: +1 section]
✓ plan.md             [1 task marked complete]

Brain synchronized.

When to Run

• After every /task completion
• After manual file changes
• Before /commit
• Before /session-end

What NOT to Update

• development_standard.md — Only changes with human approval
• history_log.md — Updated at session-end only

Section Status Tracking

In codebase_index.md, track sections within pages:

**Current State:**
- ✓ Section name (complete)
- → Section name (in progress)
- ○ Section name (pending)

This gives visibility into partial page completion.