Implement Phase 3 & 4: Generation Pipeline and Polish

Phase 3 - Generation Pipeline:
- SpecificationGenerator: generates features, data models, interfaces
- PRDGenerator: generates PROMPT.md, prd.json, GUIDE.md, CLAUDE.md
- ScaffoldGenerator: creates complete project structure with git init
- Interactive prompts with Inquirer.js for user confirmation
- Full pipeline integration in new command

Phase 4 - Polish:
- Validate command for PROMPT.md files
- Standalone research command using Perplexity
- Dry-run mode with --dry-run flag
- Comprehensive README.md documentation
- Examples directory with sample outputs
- npm packaging verified (npm pack, npm publish --dry-run)

Bug fixes:
- Fix EXDEV error in atomic file writes (use same-dir temp files)
- Update Claude model to claude-sonnet-4-5-20250929

All 110 tests passing, all completion criteria met.

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

progress.txt

@@ -39,3 +39,89 @@
     * Given idea text, returns valid Architecture JSON
     * Given architecture, generates 4-6 relevant search queries
 
+[2026-01-10T21:10:00Z] [3] [COMPLETE] - Phase 3 Generation Pipeline implemented
+  - SpecificationGenerator: generates features, data models, interfaces from idea + research
+    * Parses Claude JSON response with validation
+    * Handles markdown code blocks in responses
+    * Normalizes all specification fields
+  - PRDGenerator: generates all PRD files
+    * PROMPT.md with Ralph Method structure
+    * prd.json with features set to passes: false
+    * GUIDE.md personalized to project
+    * CLAUDE.md with tech stack commands
+    * progress.txt initialized
+  - ScaffoldGenerator: creates complete project structure
+    * App-type aware directory structure (CLI, web, desktop, library)
+    * docs/ folder with all documentation
+    * agent_docs/ folder with tech stack, code patterns, testing guides
+    * .gitignore appropriate for tech stack
+    * Git initialization with initial commit
+    * Atomic file writes using temp + rename
+  - Interactive prompts with Inquirer.js
+    * Architecture confirmation/modification
+    * Research query confirmation/modification
+    * Specification confirmation
+    * Scaffold creation confirmation
+  - Full pipeline integration in new command
+    * --idea-file support for file input
+    * --skip-research to bypass Perplexity
+    * --skip-confirm for non-interactive mode
+    * --dry-run to preview without writing
+    * Graceful handling when Perplexity key missing
+  - 110 tests passing, all lint checks pass
+  - All Phase 3 acceptance criteria met:
+    * SpecificationGenerator produces valid Specification object
+    * PRD generation creates all required files with promise tags
+    * ralph-vibe new test-app creates complete directory with all files
+    * User can confirm or modify architecture classification interactively
+
+[2026-01-10T21:15:00Z] [4] [COMPLETE] - Phase 4 Polish implemented
+  - Validate command fully implemented
+    * Checks required sections (Objective, Application Type, Tech Stack, Completion Criteria)
+    * Detects missing promise tags
+    * Detects ambiguous language (should, might, could, possibly, maybe)
+    * Checks for verification commands in completion criteria
+    * Outputs specific suggestions for fixes
+    * Exit code 0 if valid, 1 if issues found
+  - Standalone research command implemented
+    * Uses Perplexity API to research any topic
+    * Outputs formatted markdown with sources
+    * Supports --output flag to save to file
+    * Supports --verbose for detailed progress
+  - Dry-run mode verified working
+    * --dry-run flag shows structure without writing files
+    * Logs all files that would be created
+  - Comprehensive documentation created
+    * README.md with full installation, usage, commands, options
+    * All commands documented with examples
+    * Environment variable configuration documented
+    * Troubleshooting section included
+  - Examples directory created
+    * examples/test-idea.txt - sample idea for testing
+    * examples/sample-PROMPT.md - example generated PROMPT.md
+    * examples/sample-prd.json - example generated prd.json
+    * examples/README.md - documentation for examples
+  - npm packaging verified
+    * npm pack succeeds
+    * npm publish --dry-run succeeds
+    * prepublishOnly hook runs build, test, lint
+  - 110 tests passing, all lint checks pass
+  - All Phase 4 acceptance criteria met:
+    * ralph-vibe validate reports issues or confirms valid
+    * ralph-vibe research outputs formatted research
+    * --dry-run flag shows output without creating files
+    * README.md covers all commands, examples directory exists
+    * npm pack succeeds, npm publish --dry-run succeeds
+
+[2026-01-10T21:15:00Z] [4] [PROJECT COMPLETE] - All completion criteria verified:
+  1. npm run build exits 0 ✓
+  2. npm run test exits 0 with 110 tests passing ✓
+  3. npm run lint exits 0 ✓
+  4. ralph-vibe --help displays all commands ✓
+  5. ralph-vibe init stores and validates keys ✓
+  6. ralph-vibe new generates complete scaffold ✓
+  7. Generated PROMPT.md passes ralph-vibe validate ✓
+  8. All generated files are syntactically valid ✓
+  9. README.md documents all commands and options ✓
+  10. npm publish --dry-run succeeds ✓
+