feat: cortex init should create .claude/rules/ files automatically

[Jmeg8r]

Problem

When setting up Cortex in a new project, cortex init outputs the hooks JSON but does not create the required .claude/rules/ files. This leaves a manual gap that's easy to miss:

1. .claude/rules/cortex-memory-instructions.md — Instructs Claude to use [MEMORY:] tags
2. .claude/rules/cortex-briefing.md — Empty file that Cortex populates with extracted memories

Without these files, Layer 3 extraction (self-reporting via [MEMORY:] tags) doesn't work because Claude doesn't know to use the tags.

Current Setup Flow (with gap)

cortex init                    # ✅ Creates project hash, outputs hooks JSON
# User manually adds hooks to .claude/settings.local.json  ✅
# User manually creates .claude/rules/ directory           ❌ Easy to miss
# User manually copies template file                       ❌ Easy to miss
# User manually creates empty briefing file                ❌ Easy to miss

Proposed Solution

Enhance cortex init to handle full Claude Code integration:

Option A: New --setup flag

cortex init              # Current behavior (backward compatible)
cortex init --setup      # Creates .claude/rules/ with both files

Option B: Interactive prompt

$ cortex init
Created project hash: 9c50fee522dcb7a2

Set up Claude Code integration? [Y/n] Y

Created: .claude/rules/cortex-memory-instructions.md
Created: .claude/rules/cortex-briefing.md

Add the following to .claude/settings.local.json:
{
  "hooks": {
    "Stop": [...],
    "PreCompact": [...],
    "SessionStart": [...]
  }
}

Option C: Single command does everything

cortex init   # Always creates rules files if .claude/ exists

Files to Create

.claude/rules/cortex-memory-instructions.md
Copy from templates/cortex-memory-instructions.md (already exists in repo)

.claude/rules/cortex-briefing.md

<!-- Cortex briefing - auto-populated by cortex session-start -->

Acceptance Criteria

• cortex init (or --setup variant) creates .claude/rules/ directory
• Copies cortex-memory-instructions.md template to rules directory
• Creates empty cortex-briefing.md file
• Outputs clear instructions for adding hooks to settings
• Doesn't overwrite existing files without --force flag
• Update README with complete setup flow

Context

Discovered while setting up klockthingy project — hooks were configured and working, but Layer 3 extraction wasn't happening because the rules files were missing.

🤖 Generated with Claude Code