Add development plan with 13 milestone specifications

- docs/plan.md: Master roadmap with phases and priorities
- docs/milestones/01-13: Detailed specs for each feature
- Updated CLAUDE.md with plan references and build commands

Milestones cover:
- Phase 1: Temporal versioning, auto-capture, context injection, codebase indexing
- Phase 2: Daily journal, content ingestion, graph visualization, import/export
- Phase 3: Multi-graph, smart retrieval, TUI dashboard, browser extension, shell completions

CLAUDE.md

@@ -1,23 +1,65 @@
-# Project Memory Guidelines
+# Cortex Development Guidelines
 
-## Before Making Changes
+## Development Plan
+
+See [docs/plan.md](docs/plan.md) for the full roadmap and milestone breakdown.
+
+### Current Phase: Core Memory System
+- [Milestone 1: Temporal Versioning](docs/milestones/01-temporal-versioning.md)
+- [Milestone 2: Auto-Capture System](docs/milestones/02-auto-capture.md)
+- [Milestone 3: Context Injection](docs/milestones/03-context-injection.md)
+- [Milestone 4: Codebase Indexing](docs/milestones/04-codebase-indexing.md)
+
+---
+
+## Project Memory Guidelines
+
+### Before Making Changes
 - **Always query memory** before modifying code or making architectural decisions: use `memory_query` to search for relevant context.
 - Use `memory_show` to check existing context on a specific topic before acting.
 - Check for existing decisions, gotchas, and component info that may affect your changes.
 
-## After Making Changes
+### After Making Changes
 - **Store new decisions** as memory nodes (kind: `decision`) when architectural choices are made.
 - **Store gotchas** as memory nodes (kind: `memory`) when you discover non-obvious behavior.
 - **Store component info** (kind: `component`) when creating or significantly modifying a module.
 - Tag nodes appropriately for future retrieval.
 
 ## Memory Tools (MCP)
-- `memory_query` — search memory by text
-- `memory_show` — show a node by ID or prefix
-- `memory_list` — list nodes filtered by kind/status/tags
-- `memory_children` — list children of a node
-- `memory_add` — add a new memory node
-- `memory_link` — create a relationship between nodes
+
+| Tool | Description |
+|------|-------------|
+| `memory_query` | Search memory by text (hybrid BM25 + vector) |
+| `memory_show` | Show a node by ID or prefix |
+| `memory_list` | List nodes filtered by kind/status/tags |
+| `memory_children` | List children of a node |
+| `memory_add` | Add a new memory node |
+| `memory_link` | Create a relationship between nodes |
+| `memory_split` | Break a large node into smaller children |
+| `memory_merge` | Merge multiple nodes into one |
+| `memory_dedupe` | Find similar/duplicate nodes |
+| `memory_prune` | Clean up stale nodes or orphans |
+| `memory_stats` | Get graph statistics |
+| `memory_summary` | Get hierarchical summary of the graph |
+| `memory_prompt` | Execute natural language instruction |
+
+## Build Commands
+
+```bash
+# Development
+npm run build          # Compile TypeScript
+npm run dev            # Watch mode
+
+# Standalone Executables
+npm run package:win    # Windows (cortex.exe + cortex-mcp.exe)
+npm run package:linux  # Linux
+npm run package:mac    # macOS
+
+# Run
+node dist/cli/index.js <command>  # Development
+./build/cortex.exe <command>      # Standalone
+```
 
 ## Git Preferences
 - Do not add `Co-Authored-By` lines to commits.
+- Keep commits focused on single milestones when possible.