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>

examples/sample-prd.json

@@ -0,0 +1,51 @@
+{
+  "project": "md2pdf",
+  "version": "1.0.0",
+  "features": [
+    {
+      "id": "basic-conversion",
+      "phase": 1,
+      "name": "Basic Conversion",
+      "description": "Convert a single markdown file to PDF",
+      "priority": 1,
+      "passes": false,
+      "acceptance": "md2pdf input.md creates input.pdf as valid PDF"
+    },
+    {
+      "id": "syntax-highlighting",
+      "phase": 2,
+      "name": "Syntax Highlighting",
+      "description": "Code blocks render with syntax highlighting",
+      "priority": 2,
+      "passes": false,
+      "acceptance": "Code blocks with language tags are highlighted correctly"
+    },
+    {
+      "id": "theme-support",
+      "phase": 2,
+      "name": "Theme Support",
+      "description": "Multiple visual themes for output",
+      "priority": 3,
+      "passes": false,
+      "acceptance": "--theme light/dark/custom works correctly"
+    },
+    {
+      "id": "table-of-contents",
+      "phase": 3,
+      "name": "Table of Contents",
+      "description": "Generate TOC from headings",
+      "priority": 4,
+      "passes": false,
+      "acceptance": "--toc flag adds clickable table of contents"
+    },
+    {
+      "id": "gfm-support",
+      "phase": 3,
+      "name": "GitHub Flavored Markdown",
+      "description": "Support GFM extensions",
+      "priority": 5,
+      "passes": false,
+      "acceptance": "Tables, task lists, and strikethrough render correctly"
+    }
+  ]
+}