memory-journal-mcp

v7.7.1

Published

6 days ago

Project context management for AI-assisted development - Persistent knowledge graphs and intelligent context recall across fragmented AI threads

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neverinfamous

mcp context-management project-management ai-assistant knowledge-graph developer-tools git github-projects model-context-protocol persistent-memory thread-continuity semantic-search sqlite typescript

Memory Journal MCP Server

🎯 AI Context + Project Intelligence: Bridge disconnected AI sessions with persistent project memory and automatic session handoff — with full GitHub workflow integration.

GitHub • Wiki • Changelog • Release Article

🚀 Quick Deploy:

npm Package - npm install -g memory-journal-mcp
Docker Hub - Alpine-based with full semantic search

🧠 Stop Experiencing AI Amnesia

When managing large projects with AI assistance, you face a critical challenge:

Thread Amnesia - Each new AI conversation starts from zero, unaware of previous work.
Lost Context - Decisions, implementations, and learnings scattered across disconnected threads.
Repeated Work - AI suggests solutions you've already tried or abandoned.
Context Overload - Manually copying project history into every new conversation.

Memory Journal solves this by acting as your project's long-term memory, bridging the gap between fragmented AI sessions.

Experience true context-aware development:

"Why did we choose SQLite over Postgres for this service last month?" (Semantic search)
"Run the /issue-triage workflow on the top priority ticket in the Kanban board." (GitHub operations)
"Who has been touching the auth module recently, and what's our team collaboration density?" (Team analytics)
"I'm stuck on this database error. Raise a 'blocker' flag for @sarah so her agent sees it next session." (Hush Protocol)
"Close issue #42 and log an entry explaining our architectural fix for the parsing bug." (Context lifecycles)
"Draw a visual graph showing how my last 10 architectural decisions relate to each other." (Knowledge graph)

See complete examples & prompts →

🎯 What Sets Us Apart

70 MCP Tools · 17 Workflow Prompts · 36 Resources · 10 Tool Groups · Code Mode · GitHub Commander (Issue Triage, PR Review, Milestone Sprints, Security/Quality/Perf Audits) · GitHub Integration (Issues, PRs, Actions, Kanban, Milestones, Insights) · Team Collaboration (Shared DB, Vector Search, Cross-Project Insights, Hush Protocol Flags)

| Feature | Description | | ----------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Session Intelligence | Agents auto-query project history, create entries at checkpoints, and hand off context between sessions via /session-summary and team-session-summary | | GitHub Integration | 18 tools for Issues, PRs, Actions, Kanban, Milestones (%), Copilot Reviews, and 14-day Insights | | Dynamic Project Routing | Seamlessly switch contexts and access CI/Issue tracking across multiple repositories using a single server instance via PROJECT_REGISTRY | | Knowledge Graphs | 8 relationship types linking specs → implementations → tests → PRs with Mermaid visualization | | Hybrid Search | Reciprocal Rank Fusion combining FTS5 keywords, semantic vector similarity, auto-heuristics, and date-range filters | | Code Mode | Execute multi-step operations in a trusted-admin execution environment — up to 90% token savings via mj.* API | | Configurable Briefing | 15 env vars / CLI flags control memory://briefing content — entries, team, GitHub detail, skills awareness, chronological grounding | | Reports & Analytics | Standups, retrospectives, PR summaries, digests, period analyses, and milestone tracking | | Hush Protocol (Flags) | Replace Slack/Teams noise with structured, actionable, and searchable AI flags (blockers, reviews) that automatically surface in session briefings | | Team Collaboration | 25 tools with full parity — CRUD, vector search, relationship graphs, cross-project insights, author attribution, Hush Protocol flags | | Data Interoperability | Bidirectional Markdown roundtripping, unified IO namespace, and schema-safe JSON exports with hard bounds-checked path traversal defenses | | Backup & Restore | One-command backup/restore with automated scheduling, retention policies, and safety-net auto-backups | | Security & Transport | OAuth 2.1 (RFC 9728/8414, JWT/JWKS, scopes), Streamable HTTP + SSE, rate limiting, CORS, SQL injection prevention, non-root Docker | | Structured Error Handling | Every tool returns {success, error, code, category, suggestion, recoverable} — agents get classification, remediation hints, and recoverability signals | | Agent Collaboration | IDE agents and Copilot share context; review findings become searchable knowledge; agents suggest reusable rules and skills (setup) | | Native Agent Skills | Bundled foundational coding paradigms (autonomous-dev, python, docker, tailwind-css, golang, playwright-standard, etc.) establishing permanent AI behavior and architecture rules | | GitHub Commander | Pipeline skills for issue triage, PR reviews, sprint milestones, and security/quality/performance audits with journal trails (docs) |

flowchart TB
    subgraph Session["🤖 AI Session Start"]
        Briefing["📋 Read Briefing<br/>(memory://briefing)"]
    end

    subgraph Core["📝 Journal Operations"]
        Create["Create Entry"]
        Retrieve["Retrieve & Search"]
        Link["Link Entries"]
    end

    subgraph Search["🔍 Hybrid Search"]
        FTS["Keyword (FTS5)"]
        Semantic["Semantic (Vector)"]
        DateRange["Date Range"]
        RRF["Reciprocal Rank Fusion"]
    end

    subgraph GitHub["🐙 GitHub Integration"]
        Issues["Issues & Milestones"]
        PRs["Pull Requests"]
        Actions["GitHub Actions"]
        Kanban["Kanban Boards"]
        Insights["Repository Insights"]
    end

    subgraph Outputs["📊 Outputs"]
        Reports["Standups & Retrospectives"]
        Graphs["Knowledge Graphs"]
        Timeline["Project Timelines"]
    end

    Session --> Core
    Core --> Search
    Core <--> GitHub
    Search --> Outputs
    GitHub --> Outputs

Suggested Rule (Add to AGENTS.md, GEMINI.md, system prompts, etc.)

🛑 MANDATORY SESSION START ROUTINE

Execute BEFORE fulfilling any user request in a new session:

TARGET: Infer repo_name from the active workspace context or user prompt. If the task is not associated with a specific project, fallback to using the generic resource without a repo name (which defaults to the first registered workspace).
FETCH: Use the MCP read_resource tool (Server: memory-journal-mcp) to read memory://briefing/{repo_name} (or memory://briefing if falling back).
- RESTRICTION: Do NOT use execute_code for this step.
ACKNOWLEDGE FLAGS: If the briefing JSON contains activeFlags (count > 0), you MUST print an alert ABOVE the table: ⚠️ **{count} active flag(s)** — review before proceeding. followed by each flag (🚩 {flag_type} → @{target_user}: {preview}).
RENDER TABLE: Parse the remaining JSON into a dense 2-column Markdown Table (Field, Value).
- RESTRICTION: NO bulleted lists inside the table. Do NOT truncate summaries or issues.
- FORMATTING: Group related properties (use <br> for line breaks).
- REQUIRED GROUPS: GitHub (Repo, Branch, CI, PRs, Insights), Issues, Entry Counts, Latest Entries/Summaries, Analytics, Milestones, Workspaces.
STOP & WAIT: Do NOT autonomously resume past tasks or start work on new issues mentioned in the session summary. The briefing is strictly for context.

Tool Filtering

[!IMPORTANT] All shortcuts and tool groups include Code Mode (mj_execute_code) by default for token-efficient operations. To exclude it, add -codemode to your filter: --tool-filter starter,-codemode

Control which tools are exposed via MEMORY_JOURNAL_MCP_TOOL_FILTER (or CLI: --tool-filter):

| Filter | Tools | Use Case | | -------------------- | ----- | ------------------------ | | full | 70 | All tools (default) | | starter | ~11 | Core + search + codemode | | essential | ~7 | Minimal footprint | | readonly | 17 | Disable all mutations | | -github | 52 | Exclude a group | | -github,-analytics | 50 | Exclude multiple groups |

Filter Syntax: shortcut or group or tool_name (whitelist mode) · -group (disable group) · -tool (disable tool) · +tool (re-enable after group disable)

Custom Selection: List individual tool names to create your own whitelist: --tool-filter "create_entry,search_entries,semantic_search"

Groups: core, search, analytics, relationships, io, admin, github, backup, team, codemode

Complete tool filtering guide →

📋 Core Capabilities

🛠️ 70 MCP Tools (10 Groups)

| Group | Tools | Description | | --------------- | ----- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | codemode | 1 | Code Mode (sandboxed code execution) 🌟 Recommended | | core | 6 | Entry CRUD, tags, test | | search | 4 | Text search, date range, semantic, vector stats | | analytics | 2 | Statistics, cross-project insights | | relationships | 2 | Link entries, visualize graphs | | io | 3 | JSON/Markdown export and File-level Markdown Data Integration Interoperability (Import/Export) | | admin | 5 | Update, delete, rebuild/add to vector index, merge tags | | github | 18 | Issues, PRs, context, Kanban, Milestones, Insights, issue lifecycle, Copilot Reviews | | backup | 4 | Backup, list, restore, cleanup | | team | 25 | CRUD, search, stats, relationships, IO (Markdown import/export), backup, vector search, cross-project insights, matrix, Hush Protocol flags (requires TEAM_DB_PATH) |

Complete tools reference →

🎯 17 Workflow Prompts

find-related - Discover connected entries via semantic similarity
prepare-standup - Daily standup summaries
prepare-retro - Sprint retrospectives
weekly-digest - Day-by-day weekly summaries
analyze-period - Deep period analysis with insights
goal-tracker - Milestone and achievement tracking
get-context-bundle - Project context with Git/GitHub/Kanban
get-recent-entries - Formatted recent entries
project-status-summary - GitHub Project status reports
pr-summary - Pull request journal activity summary
code-review-prep - Comprehensive PR review preparation
pr-retrospective - Completed PR analysis with learnings
actions-failure-digest - CI/CD failure analysis
project-milestone-tracker - Milestone progress tracking
confirm-briefing - Acknowledge session context to user
session-summary - Create a session summary entry with accomplishments, pending items, and next-session context
team-session-summary - Create a retrospective team session summary entry securely isolated to the team database

Complete prompts guide →

📡 36 Resources (27 Static + 9 Template)

Static Resources (appear in resource lists):

memory://briefing - Session initialization: compact context for AI agents (~300 tokens) — includes localTime and optional activeFlags
memory://instructions - Behavioral guidance: complete server instructions for AI agents
memory://recent - 10 most recent entries
memory://significant - Significant milestones and breakthroughs
memory://graph/recent - Live Mermaid diagram of recent relationships
memory://health - Server health & diagnostics
memory://graph/actions - CI/CD narrative graph
memory://actions/recent - Recent workflow runs
memory://tags - All tags with usage counts
memory://statistics - Journal statistics
memory://rules - User rules file content for agent awareness
memory://workflows - Available agent workflows summary
memory://skills - Agent skills index (names, paths, excerpts)
memory://github/status - GitHub repository status overview
memory://github/insights - Repository stars, forks, and 14-day traffic summary
memory://github/milestones - Open milestones with completion percentages
memory://team/recent - Recent team entries with author attribution
memory://team/statistics - Team entry counts, types, and author breakdown
memory://help - Tool group index with descriptions and tool counts
memory://help/gotchas - Field notes, edge cases, and critical usage patterns
memory://metrics/summary - Aggregate tool call metrics since server start (calls, errors, token estimates, duration) — HIGH priority
memory://metrics/tokens - Per-tool token usage breakdown sorted by output token cost — MEDIUM priority
memory://metrics/system - Process-level metrics: memory (MB), uptime (s), Node.js version, platform — MEDIUM priority
memory://metrics/users - Per-user call counts (populated when OAuth user identifiers are present) — LOW priority
memory://audit - Last 50 write/admin tool call entries from the JSONL operational telemetry log (requires AUDIT_LOG_PATH)
memory://flags - Active (unresolved) team flags dashboard (requires TEAM_DB_PATH)
memory://flags/vocabulary - Configured flag vocabulary terms

Template Resources (require parameters, fetch directly by URI):

memory://projects/{number}/timeline - Project activity timeline
memory://issues/{issue_number}/entries - Entries linked to issue
memory://prs/{pr_number}/entries - Entries linked to PR
memory://prs/{pr_number}/timeline - Combined PR + journal timeline
memory://kanban/{project_number} - GitHub Project Kanban board
memory://kanban/{project_number}/diagram - Kanban Mermaid visualization
memory://milestones/{number} - Milestone detail with completion progress
memory://help/{group} - Per-group tool reference with parameters and annotations
memory://briefing/{repo} - Context targeted to a specific repository

Note: The memory://github/status, memory://github/insights, memory://github/milestones, and memory://milestones/{number} resources also accept an optional /{repo} path suffix for cross-repo targeting.

⚡ Code Mode: Maximum Efficiency (90% Token Savings)

Code Mode (mj_execute_code) is a revolutionary approach that dramatically reduces token usage by up to 90% and is included by default in all presets. Instead of spending thousands of tokens on sequential tool calls, AI agents use a single sandboxed execution to reason faster.

Code executes in a worker_threads sandbox designed as a secure multi-tenant process isolation environment. All mj.* API calls execute against the journal within the sandbox, providing:

Static code validation — blocked patterns include require(), process, eval(), and filesystem access
Rate limiting — 60 executions per minute per client
Hard timeouts — configurable execution limit (default 30s)
Full API access — all 10 tool groups are available via mj.* (e.g., mj.core.createEntry(), mj.search.searchEntries(), mj.github.getGithubIssues(), mj.team.passTeamFlag())
Strict Readonly Contract — Calling any mutation method under --tool-filter readonly safely halts the sandbox to prevent execution, returning a structured { success: false, error: "..." } response to the agent instead of a raw MCP protocol exception.

⚡ Code Mode Only (Maximum Token Savings)

Run with only Code Mode enabled — a single tool that provides access to all 69 tools' worth of capability through the mj.* API:

{
  "mcpServers": {
    "memory-journal-mcp": {
      "command": "memory-journal-mcp",
      "args": ["--tool-filter", "codemode"]
    }
  }
}

This exposes just mj_execute_code. The agent writes JavaScript against the typed mj.* SDK — composing operations across all 10 tool groups and returning exactly the data it needs — in one execution. This mirrors the Code Mode pattern pioneered by Cloudflare for their entire API: fixed token cost regardless of how many capabilities exist.

Disabling Code Mode

If you prefer individual tool calls, exclude codemode:

{
  "args": ["--tool-filter", "starter,-codemode"]
}

🤫 Hush Protocol: Asynchronous Team Collaboration

The Hush Protocol reimagines team collaboration for AI-augmented workflows by replacing noisy Slack/Teams messages with structured, machine-actionable flags.

When you encounter a blocker, need a review, or want to broadcast a milestone, your AI agent can raise a flag in the shared Team Database:

Actionable Visibility: Active flags automatically surface at the very top of the memory://briefing payload for all team members. When another developer's agent starts a session, it immediately sees your blockers and can help resolve them autonomously.
Structured Types: Raise specific flag types (blocker, needs_review, help_requested, fyi). You can customize your team's vocabulary via the --flag-vocabulary configuration.
Searchable History: Unlike chat messages that disappear into the void, Hush flags are permanent, query-able AI journal entries. Your agents can search past needs_review flags to understand how architectural blockers were conquered.

Dashboard & Operations: Read memory://flags to see an active dashboard overview and use mj.team.passTeamFlag() / mj.team.resolveTeamFlag() to manage them programmatically in Code Mode.

Complete Hush Protocol guide and Mermaid sequence diagrams →

🚀 Quick Start

Option 1: npm (Recommended)

npm install -g memory-journal-mcp

Option 2: From Source

git clone https://github.com/neverinfamous/memory-journal-mcp.git
cd memory-journal-mcp
npm install
npm run build

Add to MCP Config

Add this to your ~/.cursor/mcp.json, Claude Desktop config, or equivalent:

Basic Configuration

{
  "mcpServers": {
    "memory-journal-mcp": {
      "command": "memory-journal-mcp",
      "env": {
        "GITHUB_TOKEN": "ghp_your_token_here",
        "PROJECT_REGISTRY": "{\"my-repo\":{\"path\":\"/path/to/your/git/repo\",\"project_number\":1}}",
        "ALLOWED_IO_ROOTS": "/path/to/your/git/repo"
      }
    }
  }
}

Advanced Configuration (Recommended)

Showcasing the full power of the server, including Multi-Project Routing, Team Collaboration, Copilot awareness, and Context Injections.

{
  "mcpServers": {
    "memory-journal-mcp": {
      "command": "memory-journal-mcp",
      "env": {
        "DB_PATH": "/path/to/your/memory_journal.db",
        "TEAM_DB_PATH": "/path/to/shared/team.db",
        "GITHUB_TOKEN": "ghp_your_token_here",
        "PROJECT_REGISTRY": "{\"my-repo\":{\"path\":\"/path/to/repo\",\"project_number\":1},\"other-repo\":{\"path\":\"/path/to/other\",\"project_number\":5}}",
        "ALLOWED_IO_ROOTS": "/path/to/repo,/path/to/other,/path/to/your/skills",
        "AUTO_REBUILD_INDEX": "true",
        "MEMORY_JOURNAL_MCP_TOOL_FILTER": "codemode",
        "CODEMODE_INTERNAL_FULL_ACCESS": "true",
        "BRIEFING_ENTRY_COUNT": "3",
        "BRIEFING_SUMMARY_COUNT": "1",
        "BRIEFING_INCLUDE_TEAM": "true",
        "BRIEFING_ISSUE_COUNT": "3",
        "BRIEFING_PR_COUNT": "3",
        "BRIEFING_PR_STATUS": "true",
        "BRIEFING_WORKFLOW_COUNT": "3",
        "BRIEFING_WORKFLOW_STATUS": "true",
        "BRIEFING_COPILOT_REVIEWS": "true",
        "RULES_FILE_PATH": "/path/to/your/RULES.md",
        "SKILLS_DIR_PATH": "/path/to/your/skills",
        "MEMORY_JOURNAL_WORKFLOW_SUMMARY": "/deploy: prod deployment | /audit: security scan",
        "AUDIT_LOG_PATH": "/path/to/your/mcp-audit.jsonl",
        "TEAM_AUTHOR": "your_username"
      }
    }
  }
}

💡 Tip: Optimize your context window! Journal entries (BRIEFING_ENTRY_COUNT) capture frequent, granular actions (e.g. bug fixes, implementation steps). Session summaries (BRIEFING_SUMMARY_COUNT) surface high-level retrospectives meant to pass strategic context continuously across distinct AI sessions. Use both appropriately to keep the agent briefing highly focused!

Variants (modify the config above):

| Variant | Change | | ----------------------- | ---------------------------------------------------------------------------------------------------------------------------- | | Minimal (no GitHub) | Remove the env block entirely | | npx (no install) | Replace "command" with "npx" and add "args": ["-y", "memory-journal-mcp"] | | From source | Replace "command" with "node" and add "args": ["dist/cli.js"] | | Code Mode only | Add "args": ["--tool-filter", "codemode"] (single tool, all capabilities) | | Docker | Replace "command" with "docker" and use run -i --rm -v ./data:/app/data writenotenow/memory-journal-mcp:latest as args | | Team collaboration | Add "TEAM_DB_PATH": "./team.db" to env |

Restart your MCP client and start journaling!

Option 3: HTTP/SSE Transport (Remote Access)

🔒 Security Posture: Stdio vs HTTP
Stdio (Default): Runs implicitly within the secure boundaries of your local IDE or command-line environment. No explicit authentication is required because the execution context is already trusted.
HTTP/SSE: Exposes the server over a network socket. By default, HTTP binds ONLY to localhost and blocks wildcard CORS to prevent unauthorized access and CSRF attacks. Public network binding (--server-host 0.0.0.0) requires explicit authentication (--auth-token or --oauth-enabled). The server will throw a fatal error if you attempt to expose it publicly without securing it.

For remote access or web-based clients, run the server in HTTP mode:

memory-journal-mcp --transport http --port 3000

To bind to all interfaces (required for containers) and enable the automated proactive analytics scheduler (e.g. daily digest), you MUST provide an authentication token:

export MCP_AUTH_TOKEN="your_secure_random_token"
memory-journal-mcp --transport http --port 3000 --server-host 0.0.0.0 --digest-interval 1440

Endpoints:

| Endpoint | Description | Mode | | ------------------------------------------- | ------------------------------------------------ | -------- | | GET / | Server info and available endpoints | Both | | POST /mcp | JSON-RPC requests (initialize, tools/call, etc.) | Both | | GET /mcp | SSE stream for server-to-client notifications | Stateful | | DELETE /mcp | Session termination | Stateful | | GET /sse | Legacy SSE connection (MCP 2024-11-05) | Stateful | | POST /messages | Legacy SSE message endpoint | Stateful | | GET /health | Health check ({ status, timestamp }) | Both | | GET /.well-known/oauth-protected-resource | RFC 9728 Protected Resource Metadata | Both |

Session Management: The server uses stateful sessions by default. Include the mcp-session-id header (returned from initialization) in subsequent requests.

OAuth 2.1 — RFC 9728/8414, JWT/JWKS, granular scopes (opt-in via --oauth-enabled)
7 Security Headers — CSP, HSTS (opt-in), X-Frame-Options, and more
Rate Limiting — 100 req/min per IP · CORS — configurable multi-origin (exact-match) · 1MB body limit
Server Timeouts — Request (120s), keep-alive (65s), headers (66s) · 404 handler · Cross-protocol guard
Build Provenance · SBOM · Supply Chain Attestations · Non-root execution

Example with curl:

Initialize session (returns mcp-session-id header):

curl -X POST http://localhost:3000/mcp \
  -H "Content-Type: application/json" \
  -H "Accept: application/json, text/event-stream" \
  -d '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-03-26","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}'

List tools (with session):

curl -X POST http://localhost:3000/mcp \
  -H "Content-Type: application/json" \
  -H "Accept: application/json, text/event-stream" \
  -H "mcp-session-id: YOUR_SESSION_ID" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}'

Stateless Mode (Serverless)

For serverless deployments (Lambda, Workers, Vercel), use stateless mode:

memory-journal-mcp --transport http --port 3000 --stateless

| Mode | Progress Notifications | Legacy SSE | Serverless | | ------------------------- | ---------------------- | ---------- | ---------- | | Stateful (default) | ✅ Yes | ✅ Yes | ⚠️ Complex | | Stateless (--stateless) | ❌ No | ❌ No | ✅ Native |

Automated Scheduling (HTTP Only)

When running in HTTP/SSE mode, enable periodic maintenance jobs with CLI flags. These jobs run in-process on setInterval — no external cron needed.

Note: These flags are ignored for stdio transport because stdio sessions are short-lived (tied to your IDE session). For stdio, use OS-level scheduling (Task Scheduler, cron) or run the backup/cleanup tools manually.

memory-journal-mcp --transport http --port 3000 \
  --backup-interval 60 --keep-backups 10 \
  --vacuum-interval 1440 \
  --rebuild-index-interval 720

| Flag | Default | Description | | -------------------------------- | ------- | -------------------------------------------------------------------- | | --backup-interval <min> | 0 (off) | Create timestamped database backups and prune old ones automatically | | --keep-backups <count> | 5 | Max backups retained during automated cleanup | | --vacuum-interval <min> | 0 (off) | Run PRAGMA optimize and flush database to disk | | --rebuild-index-interval <min> | 0 (off) | Full vector index rebuild to maintain semantic search quality |

Each job is error-isolated — a failure in one job won't affect the others. Scheduler status (last run, result, next run) is visible via memory://health.

GitHub Integration Configuration

The GitHub tools (get_github_issues, get_github_prs, etc.) auto-detect the repository from your git context when PROJECT_REGISTRY is configured or the MCP server is run inside a git repository.

| Environment Variable | --------------------------------- | DB_PATH | TEAM_DB_PATH | TEAM_AUTHOR | GITHUB_TOKEN | DEFAULT_PROJECT_NUMBER | PROJECT_REGISTRY | AUTO_REBUILD_INDEX | MCP_HOST | MCP_AUTH_TOKEN | ALLOWED_IO_ROOTS | MCP_CORS_ORIGIN | MCP_RATE_LIMIT_MAX | LOG_LEVEL | MCP_ENABLE_HSTS | OAUTH_ENABLED | OAUTH_ISSUER | OAUTH_AUDIENCE | OAUTH_JWKS_URI | OAUTH_CLOCK_TOLERANCE | CODE_MODE_MAX_RESULT_SIZE | CODEMODE_INTERNAL_FULL_ACCESS | BRIEFING_ENTRY_COUNT | BRIEFING_SUMMARY_COUNT | BRIEFING_INCLUDE_TEAM | BRIEFING_ISSUE_COUNT | BRIEFING_PR_COUNT | BRIEFING_PR_STATUS | BRIEFING_MILESTONE_COUNT | BRIEFING_WORKFLOW_COUNT | BRIEFING_WORKFLOW_STATUS | BRIEFING_COPILOT_REVIEWS | RULES_FILE_PATH | SKILLS_DIR_PATH | MEMORY_JOURNAL_WORKFLOW_ | INSTRUCTION_LEVEL | PROJECT_LINT_CMD | PROJECT_TYPECHECK_CMD | PROJECT_BUILD_CMD | PROJECT_TEST_CMD | PROJECT_E2E_CMD | PROJECT_PACKAGE_MANAGER | PROJECT_HAS_DOCKERFILE | COMMANDER_HITL_FILE_THRESHOLD | COMMANDER_SECURITY_TOOLS | COMMANDER_BRANCH_PREFIX | AUDIT_LOG_PATH | AUDIT_REDACT | AUDIT_READS | AUDIT_LOG_MAX_SIZE | MCP_METRICS_ENABLED | FLAG_VOCABULARY | Description | | ----------------------------------------------------------------------------------------------------------------------------------------------------- | | Database file location (CLI: --db; default: ./memory_journal.db) | | Team database file location (CLI: --team-db) | | Override author name for team entries (default: git config user.name) | | GitHub personal access token for API access | | Default GitHub Project number for auto-assignment when creating issues | | JSON map of repos to { path, project_number } for multi-project auto-detection and routing | | Set to true to rebuild vector index on server startup | | Server bind host (0.0.0.0 for containers, default: localhost) | | Bearer token for HTTP transport authentication (CLI: --auth-token). Must NOT be the default placeholder token. | | Critical Security Boundary: Comma-separated absolute paths granting filesystem access to Code Mode and export tools (default: none / fail-closed) | | Allowed CORS origins for HTTP transport, comma-separated (default: blank, strict opt-in) | | Max requests per minute per client IP, HTTP only (default: 100) | | Log verbosity: error, warn, info, debug (default: info; CLI: --log-level) | | Enable HSTS security header on HTTP responses (CLI: --enable-hsts; default: false) | | Set to true to enable OAuth 2.1 authentication (HTTP only) | | OAuth issuer URL (e.g., https://auth.example.com/realms/mcp) | | Expected JWT audience claim | | JWKS endpoint for token signature verification | | Allowed clock skew tolerance in seconds for JWT verification (default: 5) | | Maximum size in bytes for mj_execute_code result payload (CLI: --codemode-max-result-size; default: 102400) | | Bypass tool filter constraints within the Code Mode sandbox (CLI: --codemode-internal-full-access; default: false) | | Journal entries in briefing (CLI: --briefing-entries; default: 3) | | Session summaries to list in briefing (CLI: --briefing-summaries; default: 1) | | Include team DB entries in briefing (true/false; default: false) | | Issues to list in briefing; 0 = count only (default: 0) | | PRs to list in briefing; 0 = count only (default: 0) | | Show PR status breakdown (open/merged/closed; default: false) | | Milestones to list in briefing; 0 = hide entirely (CLI: --briefing-milestones; default: 3) | | Workflow runs to list in briefing; 0 = status only (default: 0) | | Show workflow status breakdown in briefing (default: false) | | Aggregate Copilot review state in briefing (default: false) | | Path to user rules file for agent awareness (CLI: --rules-file) | | Path to skills directory for agent awareness (CLI: --skills-dir) | SUMMARY | Free-text workflow summary for memory://workflows (CLI: --workflow-summary) | | Briefing depth: essential, standard, full (CLI: --instruction-level; default: standard) | | Project lint command for GitHub Commander validation gates (default: npm run lint) | | Project typecheck command (default: npm run typecheck; empty = skip) | | Project build command (default: npm run build; empty = skip) | | Project test command (default: npm run test) | | Project E2E test command (default: empty = skip) | | Package manager override: npm, yarn, pnpm, bun (default: auto-detect from lockfile) | | Enable Docker audit steps (default: auto-detect) | | Human-in-the-loop checkpoint if changes touch > N files (default: 10) | | Override security tool auto-detection (comma-separated; default: auto-detect) | | Branch naming prefix for PRs (default: fix) | | Path for the JSONL operational telemetry log of write/admin tool calls. Rotates at 10 MB (keeps 5 archives). Omit to disable telemetry logging. | | Set to false to include tool arguments in telemetry log entries (default: true) | | Log read-scoped tool calls in addition to write/admin (CLI: --audit-reads; default: false) | | Maximum operational telemetry file size in bytes before rotation (CLI: --audit-log-max-size; default: 10485760) | | Set to false to disable in-memory tool call metrics accumulation (default: true) | | Comma-separated flag types for Hush Protocol (CLI: --flag-vocabulary; default: blocker,needs_review,help_requested,fyi) |

Multi-Project Workflows: For agents to seamlessly support multiple projects, provide PROJECT_REGISTRY.

Dynamic Context Resolution & Auto-Detection

When executing GitHub tools (issues, PRs, context, etc.), the server resolves repository context in this order:

Dynamic Project Routing: If the agent passes a repo string that matches a key in your PROJECT_REGISTRY, the server dynamically mounts the physical directory mapped to that project. It executes git commands locally and automatically infers the owner.
Explicit Override: If the agent provides both owner and repo explicitly, those values override auto-detection for API calls.
Missing Context: Without PROJECT_REGISTRY or explicit parameters, the server blocks execution and returns {requiresUserInput: true} to prompt the agent.

Automatic Project Routing (Kanban / Issues)

When opening an issue or viewing/moving a Kanban card, the server needs a GitHub Project number. It determines this via:

Exploring the raw project_number argument passed by the agent.
Checking if the repo string precisely matches an entry in your PROJECT_REGISTRY, seamlessly mapping it to its pre-configured project_number.
Falling back to the globally defined DEFAULT_PROJECT_NUMBER if set.

🔐 OAuth 2.1 Authentication

For production deployments, enable OAuth 2.1 authentication on the HTTP transport:

| Component | Status | Description | | --------------------------- | ------ | ------------------------------------------------ | | Protected Resource Metadata | ✅ | RFC 9728 /.well-known/oauth-protected-resource | | Auth Server Discovery | ✅ | RFC 8414 metadata discovery with caching | | Token Validation | ✅ | JWT validation with JWKS support | | Scope Enforcement | ✅ | Granular read, write, admin scopes | | HTTP Transport | ✅ | Streamable HTTP with OAuth middleware |

Supported Scopes:

| Scope | Tool Groups | | ------- | ------------------------------------------------- | | read | core, search, analytics, relationships, io | | write | github, team (+ all read groups) | | admin | admin, backup, codemode (+ all write/read groups) |

Quick Start:

memory-journal-mcp --transport http --port 3000 \
  --oauth-enabled \
  --oauth-issuer https://auth.example.com/realms/mcp \
  --oauth-audience memory-journal-mcp \
  --oauth-jwks-uri https://auth.example.com/realms/mcp/protocol/openid-connect/certs

Or via environment variables:

export OAUTH_ENABLED=true
export OAUTH_ISSUER=https://auth.example.com/realms/mcp
export OAUTH_AUDIENCE=memory-journal-mcp
export OAUTH_CLOCK_TOLERANCE=5
memory-journal-mcp --transport http --port 3000

Note: OAuth is opt-in. When not enabled, the server falls back to simple token authentication via MCP_AUTH_TOKEN environment variable, or runs without authentication.

🔄 Session Management

Session start → agent reads memory://briefing (or memory://briefing/{repo}) and shows project context
Session summary → use /session-summary to capture progress and next-session context
Next session's briefing includes the previous summary — context flows seamlessly

🔧 Configuration

GitHub Integration (Optional)

export GITHUB_TOKEN="your_token"              # For Projects/Issues/PRs

Scopes: repo, project, read:org (org-level project discovery only)

GitHub Management Capabilities

Memory Journal provides a hybrid approach to GitHub management:

| Capability Source | Purpose | | ------------------ | ------------------------------------------------------------------------------------------ | | MCP Server | Specialized features: Kanban visualization, Milestones, journal linking, project timelines | | Agent (gh CLI) | Full GitHub mutations: create/close issues, create/merge PRs, manage releases |

MCP Server Tools (Read + Kanban + Milestones + Issue Lifecycle):

get_github_issues / get_github_issue - Query issues
get_github_prs / get_github_pr - Query pull requests
get_github_context - Full repository context
get_kanban_board / add_kanban_item / move_kanban_item / delete_kanban_item - Kanban management
get_github_milestones / get_github_milestone - Milestone tracking with completion %
create_github_milestone / update_github_milestone / delete_github_milestone - Milestone CRUD
get_repo_insights - Repository traffic & analytics (stars, clones, views, referrers, popular paths)
create_github_issue_with_entry / close_github_issue_with_entry - Issue lifecycle with journal linking

Why this design? The MCP server focuses on value-added features that integrate journal entries with GitHub (Kanban views, Milestones, timeline resources, context linking). Standard GitHub mutations (create/close issues, merge PRs, manage releases) are handled directly by agents via gh CLI.

Complete GitHub integration guide →

GitHub Commander Workflows

The server natively bundles the github-commander agent skill (accessible via memory://skills/github-commander). This extends your AI assistant with 9 autonomous DevOps workflows for repository stewardship: Issue Triage, Milestone Sprints, PR Reviews, Copilot Audits, Security Audits, Code Quality Audits, Performance Audits, Roadmap Kickoffs, and Dependency Updates. Configure validation layers using the PROJECT_* environment overrides to enforce CI-matching execution locally during agent tasks!

🏗️ Architecture

Data Flow

flowchart TB
    AI["🤖 AI Agent<br/>(Cursor, Windsurf, Claude)"]

    subgraph MCP["Memory Journal MCP Server"]
        Tools["🛠️ 70 Tools"]
        Resources["📡 36 Resources"]
        Prompts["💬 17 Prompts"]
    end

    subgraph Storage["Persistence Layer"]
        SQLite[("💾 SQLite<br/>Entries, Tags, Relationships")]
        Vector[("🔍 Vector Index<br/>Semantic Embeddings")]
        Backups["📦 Backups"]
    end

    subgraph External["External Integrations"]
        GitHub["🐙 GitHub API<br/>Issues, PRs, Actions"]
        Kanban["📋 Projects v2<br/>Kanban Boards"]
    end

    AI <-->|"MCP Protocol"| MCP
    Tools --> Storage
    Tools --> External
    Resources --> Storage
    Resources --> External

Stack

┌─────────────────────────────────────────────────────────────┐
│ MCP Server Layer (TypeScript)                               │
│  ┌─────────────────┐  ┌─────────────────┐  ┌─────────────┐  │
│  │ Tools (70)      │  │ Resources (36)  │  │ Prompts (17)│  │
│  │ with Annotations│  │ with Annotations│  │             │  │
│  └─────────────────┘  └─────────────────┘  └─────────────┘  │
├─────────────────────────────────────────────────────────────┤
│ Native SQLite Engine                                        │
│  ┌─────────────────┐  ┌─────────────────┐  ┌─────────────┐  │
│  │ better-sqlite3  │  │ sqlite-vec      │  │ transformers│  │
│  │ (High-Perf I/O) │  │ (Vector Index)  │  │ (Embeddings)│  │
│  └─────────────────┘  └─────────────────┘  └─────────────┘  │
├─────────────────────────────────────────────────────────────┤
│ SQLite Database with Hybrid Search                          │
│  ┌─────────────────────────────────────────────────────────┐│
│  │ entries + tags + relationships + embeddings + backups   ││
│  └─────────────────────────────────────────────────────────┘│
└─────────────────────────────────────────────────────────────┘

🔧 Technical Highlights

Performance & Portability

TypeScript + Native SQLite - High-performance better-sqlite3 with synchronous I/O
sqlite-vec - Vector similarity search via SQLite extension
@huggingface/transformers - Local ML embedding models in JavaScript
Background Warmup - Model weights (~23MB) are loaded into memory asynchronously on server startup to avoid first-request latency. If the server is invoked before warmup completes, the first semantic search or vector insertion will incur a network-bound cold start (~1.5s - 3s) while the weights are cached locally.

Performance Benchmarks

Memory Journal is designed for extremely low overhead during AI task execution. We include a vitest bench suite to maintain these baseline guarantees:

Database Reads: Operations execute in fractions of a millisecond. calculateImportance is ~13-14x faster than retrieving 50 recent entries.
Vector Search Engine: Both search (~140-220 ops/sec) and indexing (~1600-1900+ ops/sec) are high-throughput via sqlite-vec with SQL-native KNN queries.
Core MCP Routines: getTools uses cached O(1) dispatch (~4800-7000x faster than get_recent_entries). create_entry and search_entries execute through the full MCP layer with sub-millisecond overhead.

To run the benchmarking suite locally:

npm run bench

Testing

Extensively tested across two frameworks:

| Suite | Command | Covers | | ------------------------- | ------------------ | ------------------------------------------------------------------------------- | | Vitest (unit/integration) | npm test | Database, tools, resources, handlers, security, GitHub, vector search, codemode | | Playwright (e2e) | npm run test:e2e | HTTP/SSE transport, auth, sessions, CORS, security headers, scheduler |

npm test          # Unit + integration tests
npm run test:e2e  # End-to-end HTTP/SSE transport tests

Security

Deterministic error handling - Every tool returns structured {success, error, code, category, suggestion, recoverable} responses with actionable context — no raw exceptions, no silent failures, no misleading messages
Local-first - All data stored locally, no external API calls (except optional GitHub)
Input validation - Zod schemas, content size limits, SQL injection prevention
Path traversal protection - Backup filenames validated
MCP 2025-03-26 annotations - Behavioral hints (readOnlyHint, destructiveHint, etc.)
HTTP transport hardening - 7 security headers, configurable multi-origin CORS, 1MB body limit, built-in rate limiting (100 req/min), server timeouts, HSTS (opt-in), 30-min session timeout, 404 handler, cross-protocol guard
Token scrubbing - GitHub tokens and credentials automatically redacted from error logs

Data & Privacy

Single SQLite file - You own your data
Portable - Move your .db file anywhere
Soft delete - Entries can be recovered
Auto-backup on restore - Never lose data accidentally

📚 Documentation & Resources

GitHub Wiki - Complete documentation
Copilot Setup Guide - Cross-agent memory bridge between IDE agents and GitHub Copilot
Deployment Guide - CI/CD pipeline, environments, and version bump checklist
Docker Hub - Container images
npm Package - Node.js distribution
Issues - Bug reports & feature requests

📄 License

MIT License - See LICENSE file for details.

🤝 Contributing

Built by developers, for developers. PRs welcome! See CONTRIBUTING.md for guidelines.

Migrating from v2.x? Your existing database is fully compatible. The TypeScript version uses the same schema and data format.