Implement Phase 1: Foundation

- Set up TypeScript project with strict mode
- Configure tsup build system (ESM output)
- Configure vitest for testing (36 tests passing)
- Configure ESLint with flat config for TypeScript
- Implement Commander.js CLI with all 4 commands:
  - init: Configure API keys with validation
  - new: Create new Ralph Method project (stub)
  - validate: Validate PROMPT.md files
  - research: Research topics via Perplexity (stub)
- Implement config management:
  - Keys stored in ~/.ralph-generator/config.json
  - File permissions set to 600
  - Environment variables override file config
- Implement logging utility with verbosity levels
- Implement atomic file writes utility

All Phase 1 acceptance criteria met.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

prd.json

@@ -8,7 +8,7 @@
       "name": "API Key Management",
       "description": "Store and retrieve API keys securely",
       "priority": 1,
-      "passes": false,
+      "passes": true,
       "acceptance": "ralph-vibe init stores keys and ralph-vibe new fails gracefully without keys"
     },
     {
@@ -17,7 +17,7 @@
       "name": "CLI Framework",
       "description": "Commander.js setup with all commands stubbed",
       "priority": 2,
-      "passes": false,
+      "passes": true,
       "acceptance": "ralph-vibe --help shows all commands, ralph-vibe init/new/validate/research exist"
     },
     {