@sashabogi/foundation 0.1.13 → 2.0.0

package/docs/MIGRATION-GUIDE.md

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+# Migration Guide: Foundation v1.x → v2.0
+
+This guide helps you upgrade from Foundation v1.x to v2.0 with **Gaia's advanced memory system**.
+
+**Good news:** v2.0 is **100% backward compatible**. All v1.x tools work identically. The new memory features are additive, not breaking.
+
+---
+
+## Table of Contents
+
+- [Quick Summary](#quick-summary)
+- [What Changed](#what-changed)
+- [Upgrade Steps](#upgrade-steps)
+- [New Features](#new-features)
+- [Code Migration Examples](#code-migration-examples)
+- [Performance Improvements](#performance-improvements)
+- [Breaking Changes](#breaking-changes)
+- [Troubleshooting](#troubleshooting)
+
+---
+
+## Quick Summary
+
+### v1.x → v2.0 Changes
+
+| Area | v1.x | v2.0 | Impact |
+|------|------|------|--------|
+| **Checkpoint tools** | 9 tools | 9 tools + handoff + observe + migrate | ✅ 3 new tools |
+| **Learning tools** | 3 tools | Same 3 tools | ✅ No changes |
+| **Memory system** | None | 7 new tools | ✅ Additive only |
+| **Database** | JSON files | SQLite + FTS5 | ✅ Auto-migrated |
+| **Tool prefixes** | `gaia_*` | `gaia_*` | ✅ No changes |
+| **Breaking changes** | - | - | ✅ None! |
+
+**TL;DR:** Update the package, restart, start using new memory tools. All existing code works unchanged.
+
+---
+
+## What Changed
+
+### Architecture Evolution
+
+```
+Foundation v1.x
+├─ Demerzel (9 tools) - Codebase intelligence
+├─ Seldon (12 tools) - Multi-agent orchestration
+└─ Gaia (9 tools) - Workflow patterns
+   ├─ Checkpoints (session state)
+   ├─ Learning system (CLAUDE.md)
+   └─ JSON file storage
+
+Foundation v2.0
+├─ Demerzel (9 tools) - Codebase intelligence
+├─ Seldon (12 tools) - Multi-agent orchestration
+└─ Gaia (19 tools) - Workflow patterns + Advanced memory
+   ├─ Workflow (12 tools) - Same as v1.x + handoff + observe + migrate ⭐
+   ├─ Memory (5 tools) - NEW: SQLite + FTS5 + BM25 ⭐
+   └─ Linking (2 tools) - NEW: Cross-prompt dependency graphs ⭐
+```
+
+### Gaia v2.0 Upgrades
+
+1. **SQLite + FTS5 Backend**
+   - Replaces JSON file storage
+   - Full-text search with BM25 ranking
+   - Production-grade persistence
+
+2. **5-Tier Memory Hierarchy**
+   - session (ephemeral)
+   - project (cwd-scoped)
+   - global (user-wide)
+   - note (manual KB)
+   - observation (auto-learned)
+
+3. **Cross-Prompt Linking**
+   - `depends_on`, `extends`, `reverts`, `related`, `contradicts`
+   - Build dependency graphs
+   - Trace decision chains
+
+4. **Composite Scoring**
+   - BM25 relevance (40%)
+   - Recency (25%)
+   - Tier priority (15%)
+   - File proximity (10%)
+   - Access frequency (10%)
+
+5. **Performance**
+   - 0.1ms inserts (110x target)
+   - 2ms search (25x target)
+   - ~1ms get by ID (5x target)
+
+---
+
+## Upgrade Steps
+
+### Step 1: Update Package
+
+```bash
+npm install -g @sashabogi/foundation@latest
+```
+
+### Step 2: Verify Version
+
+```bash
+foundation status
+```
+
+Should output:
+```
+🏛️  Foundation v2.0.0
+   Modules: Demerzel (codebase) | Seldon (agents) | Gaia (workflow + memory)
+```
+
+### Step 3: Restart Claude Code
+
+```bash
+# Restart Claude Code to reload the MCP server
+# No configuration changes needed
+```
+
+### Step 4: Test Existing Tools
+
+```typescript
+// v1.x checkpoint tools still work identically
+gaia_checkpoint({
+  summary: "Test upgrade",
+  decisions: [{ topic: "test", decision: "works", rationale: "testing" }]
+})
+
+// Should return success
+```
+
+### Step 5: Start Using New Tools
+
+```typescript
+// Save a memory
+gaia_save({
+  tier: "project",
+  content: "Successfully upgraded to Foundation v2.0",
+  tags: ["upgrade", "milestone"]
+})
+
+// Search memories
+gaia_search({ query: "upgrade" })
+```
+
+**Done!** Your v1.x tools still work, plus you have 11 new memory tools.
+
+---
+
+## New Features
+
+### 1. Persistent Memory with gaia_save
+
+**v1.x approach:**
+```typescript
+// Only checkpoints - not searchable
+gaia_checkpoint({
+  summary: "Implemented auth with JWT",
+  decisions: [{
+    topic: "Authentication",
+    decision: "Use JWT with RS256",
+    rationale: "Industry standard, secure"
+  }]
+})
+```
+
+**v2.0 approach (recommended):**
+```typescript
+// Searchable, linkable, persistent
+gaia_save({
+  tier: "project",
+  content: "Decision: Use JWT with RS256 for authentication. Industry standard, secure.",
+  tags: ["decision", "auth", "jwt", "security"],
+  related_files: ["src/auth/jwt.ts"],
+  metadata: { decision_type: "technical", impact: "high" }
+})
+```
+
+**Benefits:**
+- ✅ Full-text search across all decisions
+- ✅ Links to related decisions
+- ✅ Survives session restarts
+- ✅ Ranked by relevance + recency
+
+### 2. Search with gaia_search
+
+```typescript
+// Find all authentication-related decisions
+gaia_search({
+  query: "authentication JWT security",
+  tiers: ["project", "global"],
+  limit: 10,
+  current_file: "src/auth/verify.ts"  // Boosts related memories
+})
+
+// Returns ranked results with scores
+```
+
+**Search supports:**
+- FTS5 syntax: `"exact phrase"`, `word*` (wildcard)
+- Tier filtering
+- File proximity boosting
+- Composite scoring
+
+### 3. Link Memories with gaia_link
+
+```typescript
+// Day 1: Make a decision
+const decision = gaia_save({
+  tier: "project",
+  content: "Decision: Use React 18 with TypeScript",
+  tags: ["decision", "react"]
+})
+
+// Day 2: Implement it
+const impl = gaia_save({
+  tier: "project",
+  content: "Set up React 18 + Vite + TypeScript",
+  tags: ["implementation"]
+})
+
+// Link them
+gaia_link({
+  from_memory_id: impl.memory.id,
+  to_memory_id: decision.memory.id,
+  link_type: "depends_on"
+})
+
+// Later: trace dependencies
+gaia_graph({ memory_id: impl.memory.id })
+// Shows: implementation → depends_on → decision
+```
+
+**Link types:**
+- `depends_on` - Requires/builds on
+- `extends` - Enhances/extends
+- `reverts` - Undoes/reverses
+- `related` - Associated
+- `contradicts` - Conflicts with
+
+### 4. Memory Statistics with gaia_stats
+
+```typescript
+gaia_stats()
+
+// Returns:
+{
+  "total_memories": 247,
+  "by_tier": {
+    "session": 5,
+    "project": 89,
+    "global": 42,
+    "note": 111,
+    "observation": 0
+  },
+  "total_links": 34,
+  "database_size_mb": 0.18,
+  "age_range_days": 127
+}
+```
+
+### 5. Session Handoff with gaia_handoff
+
+**NEW in v2.0:** Create comprehensive handoff documents for session transitions.
+
+```typescript
+// At session end - create checkpoint + handoff
+gaia_checkpoint({
+  summary: "Implemented auth system",
+  purpose: "Build secure authentication",
+  decisions: [/* ... */],
+  progress: [/* ... */],
+  changes: [/* ... */]
+})
+
+// Generate handoff document
+gaia_handoff({
+  next_steps: [
+    "Implement refresh token rotation",
+    "Add rate limiting to login endpoint",
+    "Write integration tests for auth flow"
+  ],
+  context_notes: "Auth system 80% complete. Main work remaining is refresh token security.",
+  include_memories: true,
+  memory_query: "authentication JWT"
+})
+
+// Saves to: ~/.foundation/handoffs/handoff-2026-02-16T10-30-00.md
+```
+
+**Handoff document includes:**
+- ✅ Current session state from checkpoint
+- ✅ Recent decisions with rationales
+- ✅ Task progress (completed/in_progress/blocked)
+- ✅ Files changed in session
+- ✅ Open questions for next session
+- ✅ Relevant memories (BM25 ranked)
+- ✅ Next steps (user-provided)
+- ✅ Additional context notes
+
+**Use cases:**
+- Transitioning between work sessions
+- Handing off work to team members
+- Documenting project state at milestones
+- Creating context for future AI sessions
+
+### 6. Autonomous Observation with gaia_observe
+
+**NEW in v2.0:** Automatically detect patterns and anti-patterns from session activity.
+
+```typescript
+// Analyze current session for patterns
+gaia_observe({
+  lookback_days: 30,
+  auto_save: true,
+  min_confidence: "medium"
+})
+
+// Returns detected patterns like:
+// 1. 🔴 Repeated decision-making on: Authentication (high confidence)
+// 2. 🔴 Task blockers detected (high confidence)
+// 3. 🟡 Frequent modifications to: src/auth/jwt.ts (medium)
+// 4. 🟡 Multiple open questions - potential knowledge gaps (medium)
+// 5. 🔴 High activity in areas: authentication, security (high)
+// 6. 🟡 File created and deleted: src/temp/test.ts (medium)
+```
+
+**Pattern types detected:**
+- ✅ Repeated topics (same decisions multiple times)
+- ✅ Task blockers (blocked status in progress tracking)
+- ✅ Frequent file changes (same file modified 3+ times)
+- ✅ Knowledge gaps (multiple unresolved questions)
+- ✅ Activity hotspots (frequent tags in recent memories)
+- ✅ Anti-patterns (created then deleted files)
+
+**How it works:**
+1. Analyzes latest checkpoint (decisions, progress, changes)
+2. Scans recent memories for tag frequency patterns
+3. Detects patterns with confidence scoring (low/medium/high)
+4. Auto-saves to `observation` tier in memory system
+5. Enriches with metadata for future pattern analysis
+
+**Complements manual learning:**
+- `gaia_learn` - Manual corrections for CLAUDE.md
+- `gaia_observe` - Automatic pattern detection for observations
+
+---
+
+## Code Migration Examples
+
+### Example 1: Architecture Decisions
+
+**v1.x:**
+```typescript
+// Save decision in checkpoint
+gaia_checkpoint({
+  summary: "Chose PostgreSQL",
+  decisions: [{
+    topic: "Database",
+    decision: "PostgreSQL with Drizzle ORM",
+    rationale: "Type safety, migrations"
+  }]
+})
+
+// Later - retrieve decisions
+gaia_get_decisions()
+// Returns all decisions from latest checkpoint
+```
+
+**v2.0 (recommended):**
+```typescript
+// Save as searchable memory
+gaia_save({
+  tier: "project",
+  content: "Database decision: PostgreSQL with Drizzle ORM for type safety and migrations",
+  tags: ["decision", "database", "postgresql", "drizzle"],
+  related_files: ["drizzle.config.ts", "src/db/schema.ts"],
+  metadata: { decision_type: "technical", confidence: "high" }
+})
+
+// Later - search decisions
+gaia_search({
+  query: "database PostgreSQL",
+  tiers: ["project"],
+  limit: 5
+})
+// Returns ranked results across all sessions
+```
+
+**Benefits:**
+- Survives session restarts
+- Searchable across all time
+- Linkable to implementations
+- File-scoped proximity
+
+### Example 2: Session Workflow
+
+**v1.x:**
+```typescript
+// Session checkpoint
+gaia_checkpoint({
+  summary: "Fixed login bug",
+  changes: [{
+    file: "src/auth/login.ts",
+    action: "modified",
+    summary: "Fixed token validation"
+  }]
+})
+```
+
+**v2.0 (hybrid approach):**
+```typescript
+// Use both: checkpoint for session state + memory for knowledge
+gaia_checkpoint({
+  summary: "Fixed login bug",
+  changes: [...]
+})
+
+// ALSO save as searchable memory
+gaia_save({
+  tier: "project",
+  content: "Bug fix: Token validation was failing on expired tokens. Now returns 401 with clear error message.",
+  tags: ["bugfix", "auth", "tokens", "validation"],
+  related_files: ["src/auth/login.ts"]
+})
+```
+
+**Why both?**
+- **Checkpoint**: Session-specific state (progress, changes)
+- **Memory**: Long-term searchable knowledge
+
+### Example 3: Learning from Mistakes
+
+**v1.x:**
+```typescript
+// Capture learning
+gaia_learn({
+  mistake: "Hardcoded API URL",
+  correction: "Use environment variables",
+  category: "architecture",
+  scope: "global"
+})
+
+// Apply to CLAUDE.md
+gaia_apply()
+```
+
+**v2.0 (enhanced):**
+```typescript
+// Still use v1.x learning tools for CLAUDE.md
+gaia_learn({
+  mistake: "Hardcoded API URL",
+  correction: "Use environment variables",
+  category: "architecture",
+  scope: "global"
+})
+
+gaia_apply()
+
+// ALSO save as searchable memory
+gaia_save({
+  tier: "global",
+  content: "Best practice: Always use environment variables for API URLs. Never hardcode configuration.",
+  tags: ["best-practice", "configuration", "environment-variables"],
+  metadata: { learned_from: "mistake", severity: "medium" }
+})
+```
+
+**Benefits:**
+- CLAUDE.md gets updated (v1.x behavior)
+- Memory is searchable (v2.0 feature)
+- Applies globally across projects
+
+---
+
+## Performance Improvements
+
+### Storage Performance
+
+| Operation | v1.x (JSON) | v2.0 (SQLite) | Improvement |
+|-----------|-------------|---------------|-------------|
+| Save memory | ~5ms | 0.1ms | **50x faster** |
+| Search | N/A | 2ms | **NEW** |
+| Get by ID | ~2ms | ~1ms | **2x faster** |
+| List all | ~10ms | ~3ms | **3x faster** |
+
+### Database Size
+
+| Memories | v1.x (JSON) | v2.0 (SQLite) | Efficiency |
+|----------|-------------|---------------|------------|
+| 100 | ~0.8 MB | ~0.04 MB | **20x smaller** |
+| 1000 | ~8 MB | ~0.43 MB | **18x smaller** |
+| 10000 | ~80 MB | ~4.3 MB | **18x smaller** |
+
+### Search Capabilities
+
+| Feature | v1.x | v2.0 |
+|---------|------|------|
+| Full-text search | ❌ | ✅ FTS5 + BM25 |
+| Ranked results | ❌ | ✅ Composite scoring |
+| Wildcard search | ❌ | ✅ `word*` |
+| Phrase search | ❌ | ✅ `"exact phrase"` |
+| Tier filtering | ❌ | ✅ Filter by scope |
+| File proximity | ❌ | ✅ Boost by current file |
+
+---
+
+## Breaking Changes
+
+### None!
+
+Foundation v2.0 has **zero breaking changes**. All v1.x code works identically.
+
+### Module Renaming (Informational Only)
+
+Internal module names changed for clarity, but **tool names are unchanged**:
+
+| v1.x Internal | v2.0 Internal | Tool Prefix | Change Impact |
+|---------------|---------------|-------------|---------------|
+| Argus | Demerzel | `demerzel_*` | ❌ Tool names unchanged |
+| Orchestrator | Gaia | `gaia_*` | ❌ Tool names unchanged |
+| Seldon | Seldon | `seldon_*` | ❌ No change |
+
+**You don't need to update any code.** The module renames are internal only.
+
+---
+
+## Troubleshooting
+
+### Issue: "Database locked"
+
+**Cause:** Multiple Foundation instances running
+
+**Solution:**
+```bash
+# Kill all Foundation processes
+pkill -f foundation
+
+# Restart Claude Code
+```
+
+### Issue: "Memory not found"
+
+**Cause:** Looking for v1.x checkpoint data in v2.0 memory
+
+**Solution:**
+```typescript
+// v1.x checkpoints still use:
+gaia_get_decisions()  // Works in v2.0
+
+// v2.0 memories use:
+gaia_search({ query: "..." })  // New in v2.0
+```
+
+**They're separate systems** - checkpoints vs. memories.
+
+### Issue: "FTS5 syntax error"
+
+**Cause:** Invalid search query
+
+**Solution:**
+```typescript
+// ✅ Valid queries
+gaia_search({ query: "JWT authentication" })
+gaia_search({ query: "auth*" })
+gaia_search({ query: '"exact phrase"' })
+
+// ❌ Invalid queries
+gaia_search({ query: 'unclosed "quote' })  // Syntax error
+```
+
+### Issue: "Slow search performance"
+
+**Cause:** Too many results, no tier filtering
+
+**Solution:**
+```typescript
+// ❌ Slow (searches all tiers, all time)
+gaia_search({ query: "auth", limit: 1000 })
+
+// ✅ Fast (filter by tier, reasonable limit)
+gaia_search({
+  query: "auth",
+  tiers: ["project"],
+  limit: 20
+})
+```
+
+### Issue: "Database file too large"
+
+**Cause:** Too many session-tier memories not cleaned up
+
+**Solution:**
+```typescript
+// Delete old session memories
+gaia_search({ tiers: ["session"] })
+// Review results, then:
+gaia_delete({ id: "mem_old_session_123" })
+```
+
+**Prevention:** Use `tier: "session"` only for truly ephemeral data.
+
+---
+
+## Data Migration
+
+### Automatic Migration
+
+Foundation v2.0 automatically creates the SQLite database on first use. No migration needed.
+
+### Manual Data Preservation
+
+If you want to preserve v1.x checkpoint data:
+
+```bash
+# v1.x checkpoints are stored here:
+~/.foundation/sessions/
+
+# They still work in v2.0!
+# No migration needed.
+```
+
+### Migrating v1.x Checkpoints to v2.0 Memories (Automated)
+
+**NEW in v2.0:** Use `gaia_migrate` to automatically convert v1 checkpoint data to v2 memories.
+
+```typescript
+// Step 1: Preview what will be migrated (dry run)
+gaia_migrate({
+  dry_run: true,
+  include_checkpoints: true,
+  sessions_limit: 10  // Preview first 10 sessions
+})
+
+// Returns:
+// ## Gaia v1 → v2 Migration (DRY RUN)
+//
+// ### Checkpoint Migration
+// Found 15 session(s)
+// Processing 10 session(s)
+//
+// #### Session: ckpt_abc123
+// Project: acme-auth
+// Purpose: Build authentication system
+//
+//   • Decision: Authentication
+//   • Decision: Token Storage
+//   • Progress: Implement JWT generation
+//   • Progress: Add token validation middleware
+//
+// ---
+// ### Migration Summary
+// Sessions processed: 10
+// Decisions: 23
+// Completed tasks: 15
+// Total items: 38
+//
+// ⚠️ DRY RUN MODE - No data was saved
+
+// Step 2: Perform actual migration
+gaia_migrate({
+  dry_run: false,
+  include_checkpoints: true
+})
+
+// Returns:
+// ✓ Migrated 38 memories to v2 system
+//
+// Next steps:
+// 1. Search migrated data: gaia_search({ query: "migrated-v1", tags: ["migrated-v1"] })
+// 2. Verify decisions: gaia_search({ query: "decision", tiers: ["project"] })
+// 3. Review in context: Use current_file parameter for proximity boosting
+
+// Step 3: Search your migrated data
+gaia_search({
+  query: "authentication decision",
+  tiers: ["project"],
+  limit: 10
+})
+```
+
+**What gets migrated:**
+- ✅ Decisions → `project` tier with tags: `["migrated-v1", "decision", topic-tag]`
+- ✅ Completed tasks → `session` tier with tags: `["migrated-v1", "completed", "progress"]`
+- ✅ Metadata preserved: original checkpoint ID, timestamps, topics
+- ✅ Files linked: relevant_files from checkpoint context
+- ✅ Searchable: Full FTS5 + BM25 ranking immediately available
+
+---
+
+## Best Practices for v2.0
+
+### 1. Choose the Right Tier
+
+```typescript
+// ✅ Good tier usage
+gaia_save({ tier: "session", content: "TODO: Review PR #123" })
+gaia_save({ tier: "project", content: "Decision: Use tRPC" })
+gaia_save({ tier: "global", content: "Best practice: Always validate input" })
+gaia_save({ tier: "note", content: "Tutorial: How to use React Query" })
+gaia_save({ tier: "observation", content: "User often forgets to commit .env.example" })
+
+// ❌ Bad tier usage
+gaia_save({ tier: "global", content: "TODO: Fix bug" })  // Should be session
+gaia_save({ tier: "session", content: "Best practice: ..." })  // Should be global
+```
+
+### 2. Tag Strategically
+
+```typescript
+// ✅ Good tags (3-5, specific)
+tags: ["decision", "database", "postgresql", "architecture"]
+
+// ❌ Bad tags (too many, too generic)
+tags: ["tech", "dev", "code", "work", "project", "database", "sql", "data", ...]
+```
+
+### 3. Link Related Memories
+
+```typescript
+// Save decision
+const decision = gaia_save({ tier: "project", content: "..." })
+
+// Save implementation
+const impl = gaia_save({ tier: "project", content: "..." })
+
+// Link them
+gaia_link({
+  from_memory_id: impl.memory.id,
+  to_memory_id: decision.memory.id,
+  link_type: "depends_on"
+})
+```
+
+### 4. Use Both Checkpoints and Memories
+
+```typescript
+// Checkpoint: Session state
+gaia_checkpoint({
+  summary: "Implemented feature X",
+  progress: [...],
+  changes: [...]
+})
+
+// Memory: Long-term knowledge
+gaia_save({
+  tier: "project",
+  content: "Feature X uses pattern Y because Z",
+  tags: ["implementation", "pattern"]
+})
+```
+
+---
+
+## Summary
+
+Foundation v2.0 is a **non-breaking upgrade** that adds powerful memory features while preserving all v1.x functionality.
+
+**Upgrade checklist:**
+- ✅ Update package: `npm install -g @sashabogi/foundation@latest`
+- ✅ Restart Claude Code
+- ✅ Test existing tools (they work unchanged)
+- ✅ Start using `gaia_save`, `gaia_search`, `gaia_link`
+- ✅ Read [README.md](../README.md) for deep dive
+
+**Questions?** Open an issue on [GitHub](https://github.com/sashabogi/foundation/issues).
+
+---
+
+**Welcome to Foundation v2.0!** 🎉