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

docs/milestones/02-auto-capture.md

@@ -0,0 +1,212 @@
+# Milestone 2: Auto-Capture System
+
+## Overview
+
+Automatically capture Claude Code conversations as memory nodes. Every significant interaction becomes searchable knowledge without manual effort.
+
+## Motivation
+
+- Manual memory creation is friction that prevents adoption
+- Conversations contain valuable context that's lost after the session
+- Supermemory's killer feature is invisible capture
+- "Just works" experience is essential for daily use
+
+## Features
+
+### 2.1 Conversation Hooks
+
+Integrate with Claude Code's hook system to capture interactions.
+
+```json
+// .claude/settings.json
+{
+  "hooks": {
+    "post_response": {
+      "command": "cortex capture-hook",
+      "timeout": 5000
+    }
+  }
+}
+```
+
+### 2.2 Smart Summarization
+
+Don't store raw conversations — summarize and extract:
+
+```typescript
+interface CapturedMemory {
+  summary: string;          // 1-2 sentence summary
+  topics: string[];         // Extracted topics/tags
+  decisions: string[];      // Any decisions made
+  codeChanges: string[];    // Files modified
+  relatedNodes: string[];   // Links to existing nodes
+}
+```
+
+### 2.3 Deduplication
+
+Prevent duplicate memories from similar conversations:
+
+- Embedding similarity check before insert
+- Merge into existing node if >0.90 similarity
+- Link as "relates_to" if 0.75-0.90 similarity
+
+### 2.4 Capture Modes
+
+```bash
+# Always capture (default when enabled)
+cortex config set capture.mode always
+
+# Only capture on explicit save
+cortex config set capture.mode manual
+
+# Capture decisions and code changes only
+cortex config set capture.mode decisions
+
+# Disable capture
+cortex config set capture.mode off
+```
+
+### 2.5 MCP Notification
+
+Add MCP tool for Claude to explicitly save memories:
+
+```typescript
+memory_capture   // Explicitly capture current context
+memory_remember  // "Remember this for later" - user triggered
+```
+
+## Implementation
+
+### Hook Handler
+
+```typescript
+// src/cli/commands/capture-hook.ts
+export async function captureHook(input: HookInput): Promise<void> {
+  const { conversation, files_changed, session_id } = input;
+
+  // Skip if disabled or trivial interaction
+  if (!shouldCapture(conversation)) return;
+
+  // Summarize with Ollama
+  const summary = await summarizeConversation(conversation);
+
+  // Extract structured data
+  const extracted = await extractMemory(conversation, summary);
+
+  // Check for duplicates
+  const existing = await findSimilar(extracted.embedding);
+
+  if (existing && existing.similarity > 0.90) {
+    // Merge into existing
+    await mergeIntoNode(existing.id, extracted);
+  } else {
+    // Create new node
+    await addNode({
+      kind: 'memory',
+      title: extracted.summary.slice(0, 100),
+      content: extracted.fullSummary,
+      tags: ['auto-capture', ...extracted.topics],
+      metadata: {
+        session_id,
+        files_changed,
+        captured_at: Date.now(),
+        source: 'claude-code'
+      }
+    });
+  }
+}
+```
+
+### Summarization Prompts
+
+```typescript
+const SUMMARIZE_PROMPT = `
+Summarize this Claude Code conversation in 1-2 sentences.
+Focus on: what was accomplished, decisions made, problems solved.
+Do NOT include greetings or meta-discussion.
+
+Conversation:
+{conversation}
+
+Summary:`;
+
+const EXTRACT_PROMPT = `
+Extract from this conversation:
+1. Main topics (as tags, lowercase, hyphenated)
+2. Decisions made (if any)
+3. Code files discussed or modified
+
+Conversation:
+{conversation}
+
+Output as JSON:
+{"topics": [], "decisions": [], "files": []}`;
+```
+
+### Configuration
+
+```typescript
+// src/core/config.ts
+interface CaptureConfig {
+  mode: 'always' | 'manual' | 'decisions' | 'off';
+  minLength: number;        // Minimum conversation length to capture
+  excludePatterns: string[]; // Regex patterns to skip
+  autoTag: boolean;         // Auto-generate tags
+  linkRelated: boolean;     // Auto-link to related nodes
+}
+```
+
+## CLI Commands
+
+| Command | Description |
+|---------|-------------|
+| `cortex capture-hook` | Hook handler (called by Claude Code) |
+| `cortex capture <text>` | Manually capture a thought |
+| `cortex capture --session` | Capture current session summary |
+| `cortex config set capture.mode <mode>` | Set capture mode |
+
+## MCP Tools
+
+| Tool | Description |
+|------|-------------|
+| `memory_capture` | Explicitly capture current context |
+| `memory_remember` | User-triggered "remember this" |
+
+## Testing
+
+- [ ] Hook receives conversation data correctly
+- [ ] Summarization produces coherent summaries
+- [ ] Deduplication prevents duplicate nodes
+- [ ] Tags are extracted accurately
+- [ ] Related nodes are linked
+- [ ] Config modes work as expected
+
+## Acceptance Criteria
+
+- [ ] Conversations auto-captured without user action
+- [ ] Summaries are concise and useful
+- [ ] No duplicate memories for repeated topics
+- [ ] Can disable/configure capture behavior
+- [ ] Works offline (queues for later if Ollama unavailable)
+- [ ] <500ms latency (non-blocking)
+
+## Estimated Effort
+
+- Hook integration: 3 hours
+- Summarization pipeline: 4 hours
+- Deduplication logic: 3 hours
+- Configuration system: 2 hours
+- MCP tools: 2 hours
+- Testing: 3 hours
+- **Total: ~17 hours**
+
+## Dependencies
+
+- Ollama for summarization (graceful fallback if unavailable)
+- Claude Code hooks system
+
+## References
+
+- [Claude-Supermemory](https://github.com/supermemoryai/claude-supermemory)
+- [Claude Code Hooks](https://docs.anthropic.com/claude-code/hooks)