feat(memory): v1.4.0 Memory System (#9)

* feat(memory): v1.4.0 baseline - memory system with explicit recording

- Add 'remember' and 'get_memory' tools for team knowledge capture
- Auto-surface memories in search_codebase and get_team_patterns
- Migrate storage to .codebase-context/ folder (auto-migrates legacy)
- Add startup validation for ROOT_PATH before migration
- Centralize constants to prevent path drift
- Remove auto-created .gitignore (document recommendation instead)
- Delete unused generate-assets scripts

Breaking: None (additive only)

* Fix lint

* Fix security audit

Author: PatrickSys

.gitignore

@@ -2,6 +2,8 @@ node_modules/
 dist/
 .codebase-index/
 .codebase-index.json
+.codebase-context/
+.codebase/
 *.log
 .DS_Store
 .env

CHANGELOG.md

@@ -1,32 +1,71 @@
 # Changelog
 
+## [Unreleased]
+
+## [1.4.0] - 2026-01-28
+
+### Added
+
+- **Memory System**: New `remember` and `get_memory` tools capture team conventions, decisions, and gotchas
+  - **Types**: `convention` | `decision` | `gotcha`
+  - **Categories**: `tooling`, `architecture`, `testing`, `dependencies`, `conventions`
+  - **Storage**: `.codebase-context/memory.json` with content-based hash IDs (commit this)
+  - **Safety**: `get_memory` truncates unfiltered results to 20 most recent
+- **Integration with `get_team_patterns`**: Appends relevant memories when category overlaps
+- **Integration with `search_codebase`**: Surfaces `relatedMemories` via keyword match in search results
+
+### Changed
+
+- **File Structure**: All MCP files now organized in `.codebase-context/` folder for cleaner project root
+  - Vector DB: `.codebase-index/` → `.codebase-context/index/`
+  - Intelligence: `.codebase-intelligence.json` → `.codebase-context/intelligence.json`
+  - Keyword index: `.codebase-index.json` → `.codebase-context/index.json`
+  - **Migration**: Automatic on server startup (legacy JSON preserved; vector DB directory moved)
+
+### Fixed
+
+- **Startup safety**: Validates `ROOT_PATH` before running migration to avoid creating directories on typo paths
+
+### Why This Feature
+
+Patterns show "what" (97% use inject) but not "why" (standalone compatibility). AGENTS.md can't capture every hard-won lesson. Decision memory gives AI agents access to the team's battle-tested rationale.
+
+**Design principle**: Tool must be self-evident without AGENTS.md rules. "Is this about HOW (record) vs WHAT (don't record)"
+
+**Inspired by**: v1.1 Pattern Momentum (temporal dimension) + memory systems research (Copilot Memory, Gemini Memory)
 
 ## [1.3.3] - 2026-01-18
 
 ### Fixed
+
 - **Security**: Resolve `pnpm audit` advisories by updating `hono` to 4.11.4 and removing the vulnerable `diff` transitive dependency (replaced `ts-node` with `tsx` for `pnpm dev`).
 
 ### Changed
+
 - **Docs**: Clarify private `internal-docs/` submodule setup, add `npx --yes` tip, document `CODEBASE_ROOT`, and list `get_indexing_status` tool.
 - **Submodule**: Disable automatic updates for `internal-docs` (`update = none`).
 
 ### Removed
+
 - **Dev**: Remove local-only `test-context.cjs` helper script.
 
 ## [1.3.2] - 2026-01-16
 
 ### Changed
+
 - **Embeddings**: Batch embedding now uses a single Transformers.js pipeline call per batch for higher throughput.
 - **Dependencies**: Bump `@modelcontextprotocol/sdk` to 1.25.2.
 
 ## [1.3.1] - 2026-01-05
 
 ### Fixed
+
 - **Auto-Heal Semantic Search**: Detects LanceDB schema corruption (missing `vector` column), triggers re-indexing, and retries search instead of silently falling back to keyword-only results.
 
 ## [1.3.0] - 2026-01-01
 
 ### Added
+
 - **Workspace Detection**: Monorepo support for Nx, Turborepo, Lerna, and pnpm workspaces
   - New utility: `src/utils/workspace-detection.ts`
   - Functions: `scanWorkspacePackageJsons()`, `detectWorkspaceType()`, `aggregateWorkspaceDependencies()`
@@ -36,13 +75,16 @@
 - **Dependency Detection**: Added `@nx/` and `@nrwl/` prefix matching for build tools
 
 ### Fixed
+
 - **detectMetadata() bug**: All registered analyzers now contribute to codebase metadata (previously only the first analyzer was called)
   - Added `mergeMetadata()` helper with proper array deduplication and layer merging
 
 ### Changed
+
 - Updated roadmap: v1.3 is now "Extensible Architecture Foundation"
 
 ### Acknowledgements
+
 Thanks to [@aolin480](https://github.com/aolin480) for accelerating the workspace detection roadmap and identifying the detectMetadata() limitation in their fork.
 
 ## 1.2.2 (2025-12-31)
@@ -55,7 +97,6 @@ Thanks to [@aolin480](https://github.com/aolin480) for accelerating the workspac
 
 ## 1.2.1 (2025-12-31)
 
-
 ### Fixed
 
 - **MCP Protocol Compatibility**: Fixed stderr output during MCP STDIO handshake for strict clients

README.md

@@ -28,54 +28,107 @@ If your environment prompts on first run, use `npx --yes ...` (or `npx -y ...`)
 - **Testing conventions** → `Jest`: 74%, `Playwright`: 6%
 - **Framework patterns** → Angular signals, standalone components, etc.
 - **Circular dependency detection** → Find toxic import cycles between files
-
+- **Memory system** → Record "why" behind choices so AI doesn't repeat mistakes
 
 ## How It Works
 
 When generating code, the agent checks your patterns first:
 
-| Without MCP | With MCP |
-|-------------|----------|
-| Uses `constructor(private svc: Service)` | Uses `inject()` (97% team adoption) |
-| Suggests `primeng/button` directly | Uses `@mycompany/ui-toolkit` wrapper |
-| Generic Jest setup | Your team's actual test utilities |
+| Without MCP                              | With MCP                             |
+| ---------------------------------------- | ------------------------------------ |
+| Uses `constructor(private svc: Service)` | Uses `inject()` (97% team adoption)  |
+| Suggests `primeng/button` directly       | Uses `@mycompany/ui-toolkit` wrapper |
+| Generic Jest setup                       | Your team's actual test utilities    |
 
 ### Tip: Auto-invoke in your rules
 
 Add this to your `.cursorrules`, `CLAUDE.md`, or `AGENTS.md`:
 
 ```
-When generating or reviewing code, use codebase-context tools to check team patterns first.
+## Codebase Context
+
+**At start of each task:** Call `get_memory` to load team conventions.
+
+**CRITICAL:** When user says "remember this" or "record this":
+- STOP immediately and call `remember` tool FIRST
+- DO NOT proceed with other actions until memory is recorded
+- This is a blocking requirement, not optional
 ```
 
 Now the agent checks patterns automatically instead of waiting for you to ask.
 
 ## Tools
 
-| Tool | Purpose |
-|------|---------|
-| `search_codebase` | Semantic + keyword hybrid search |
-| `get_component_usage` | Find where a library/component is used |
-| `get_team_patterns` | Pattern frequencies + canonical examples |
-| `get_codebase_metadata` | Project structure overview |
-| `get_indexing_status` | Indexing progress + last stats |
-| `get_style_guide` | Query style guide rules |
-| `detect_circular_dependencies` | Find import cycles between files |
-| `refresh_index` | Re-index the codebase |
+| Tool                           | Purpose                                       |
+| ------------------------------ | --------------------------------------------- |
+| `search_codebase`              | Semantic + keyword hybrid search              |
+| `get_component_usage`          | Find where a library/component is used        |
+| `get_team_patterns`            | Pattern frequencies + canonical examples      |
+| `get_codebase_metadata`        | Project structure overview                    |
+| `get_indexing_status`          | Indexing progress + last stats                |
+| `get_style_guide`              | Query style guide rules                       |
+| `detect_circular_dependencies` | Find import cycles between files              |
+| `remember`                     | Record memory (conventions/decisions/gotchas) |
+| `get_memory`                   | Query recorded memory by category/keyword     |
+| `refresh_index`                | Re-index the codebase                         |
+
+## File Structure
+
+The MCP creates the following structure in your project:
+
+```
+.codebase-context/
+  ├── memory.json         # Team knowledge (commit this)
+  ├── intelligence.json   # Pattern analysis (generated)
+  ├── index.json          # Keyword index (generated)
+  └── index/              # Vector database (generated)
+```
+
+**Recommended `.gitignore`:** The vector database and generated files can be large. Add this to your `.gitignore` to keep them local while sharing team memory:
 
+```gitignore
+# Codebase Context MCP - ignore generated files, keep memory
+.codebase-context/*
+!.codebase-context/memory.json
+```
+
+### Memory System
+
+Patterns tell you _what_ the team does ("97% use inject"), but not _why_ ("standalone compatibility"). Use `remember` to capture rationale that prevents repeated mistakes:
+
+```typescript
+// AI won't change this again after recording the decision
+remember({
+  type: 'decision',
+  category: 'dependencies',
+  memory: 'Use node-linker: hoisted, not isolated',
+  reason:
+    "Some packages don't declare transitive deps. Isolated forces manual package.json additions."
+});
+```
+
+Memories surface automatically in `search_codebase` results and `get_team_patterns` responses.
+
+**Early baseline — known quirks:**
+
+- Agents may bundle multiple things into one entry
+- Duplicates can happen if you record the same thing twice
+- Edit `.codebase-context/memory.json` directly to clean up
+- Be explicit: "Remember this: use X not Y"
 
 ## Configuration
 
-| Variable | Default | Description |
-|----------|---------|-------------|
-| `EMBEDDING_PROVIDER` | `transformers` | `openai` (fast, cloud) or `transformers` (local, private) |
-| `OPENAI_API_KEY` | - | Required if provider is `openai` |
-| `CODEBASE_ROOT` | - | Project root to index (CLI arg takes precedence) |
-| `CODEBASE_CONTEXT_DEBUG` | - | Set to `1` to enable verbose logging (startup messages, analyzer registration) |
+| Variable                 | Default        | Description                                                                    |
+| ------------------------ | -------------- | ------------------------------------------------------------------------------ |
+| `EMBEDDING_PROVIDER`     | `transformers` | `openai` (fast, cloud) or `transformers` (local, private)                      |
+| `OPENAI_API_KEY`         | -              | Required if provider is `openai`                                               |
+| `CODEBASE_ROOT`          | -              | Project root to index (CLI arg takes precedence)                               |
+| `CODEBASE_CONTEXT_DEBUG` | -              | Set to `1` to enable verbose logging (startup messages, analyzer registration) |
 
 ## Performance Note
 
 This tool runs **locally** on your machine using your hardware.
+
 - **Initial Indexing**: The first run works hard. It may take several minutes (e.g., ~2-5 mins for 30k files) to compute embeddings for your entire codebase.
 - **Caching**: Subsequent queries are instant (milliseconds).
 - **Updates**: Currently, `refresh_index` re-scans the codebase. True incremental indexing (processing only changed files) is on the roadmap.

package.json

@@ -1,6 +1,6 @@
 {
   "name": "codebase-context",
-  "version": "1.3.3",
+  "version": "1.4.0",
   "description": "MCP server that helps AI agents understand your codebase - patterns, libraries, architecture, monorepo support",
   "type": "module",
   "main": "./dist/lib.js",
@@ -92,7 +92,7 @@
     "@xenova/transformers": "^2.17.0",
     "fuse.js": "^7.0.0",
     "glob": "^10.3.10",
-    "hono": "4.11.4",
+    "hono": "4.11.7",
     "ignore": "^5.3.1",
     "typescript": "^5.3.3",
     "uuid": "^9.0.1",