
Persistent memory for AI coding agents via MCP — a bitemporal knowledge graph of your codebase
Persistent memory for AI coding agents via MCP — a bitemporal knowledge graph of your codebase, served to Claude Code, Cursor, Gemini CLI, and any MCP client. Tree-sitter + Gemini Flash → Neo4j (via Graphiti). 12 MCP tools, hierarchical clusters, two-regime confidence decay.
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A protocol-neutral engineering-context layer for AI coding agents. memex builds a bitemporal knowledge graph of your repository — modules, symbols, decisions, problems, evidence, and code evolution — and exposes bounded, provenance-aware context through Hermes MemoryProvider or MCP.
A daemon and MCP server that turns commits and file changes into structured engineering knowledge. Agents can receive relevant repository context before a task, with freshness and provenance preserved, without making memex a source of personal memory or raw session state.
flowchart LR
A[Your repository<br/>files + git] --> B[memex watcher<br/>tree-sitter + Gemini]
B --> C[Neo4j graph<br/>bitemporal facts]
C --> D[memex core<br/>ContextPacket selection]
D --> E[Hermes MemoryProvider<br/>automatic read-only prefetch]
D --> F[MCP fallback<br/>explicit lookup]
E --> G[AI coding agent]
F --> G
style B fill:#cfe8ff,stroke:#0066cc,color:#000
style C fill:#fff4cf,stroke:#cc9900,color:#000
style E fill:#d4f5d4,stroke:#2d8f2d,color:#000/plugin marketplace add STiFLeR7/claude-plugins
/plugin install memex-mcp@stifler-marketplaceRestart your Claude Code session.
docker compose -f docker/docker-compose.yml up -d
cat > .env <<EOF
NEO4J_URI=bolt://localhost:7687
NEO4J_USER=neo4j
NEO4J_PASSWORD=memex-local
GEMINI_API_KEY=your-key-here
EOF
npx stifler-memex-mcp init --repo .
npx stifler-memex-mcp watch --repo .
npx stifler-memex-mcp serve --repo .The v0.9 Hermes integration is read-only. Hermes retains personal memory, raw
session state, and execution state. memex supplies repository engineering
context through a bounded ContextPacket; it does not ingest Hermes
state.db, transcripts, prompts, or tool results.
Add the memex provider to Hermes' profile configuration:
memory:
provider: memex
plugins:
memex:
repo_path: /absolute/path/to/repository
prefetch_timeout_seconds: 7
max_items: 8
max_chars: 12000If Hermes is not installed, use the same context selector through the MCP
get_engineering_context tool. Both paths share the protocol-neutral memex
core and fail open when retrieval is unavailable.
| Channel | Command |
|---|---|
| Claude Code marketplace | /plugin install memex-mcp@stifler-marketplace |
| npx (no install) | npx stifler-memex-mcp <cmd> |
| uv | uv add memex-mcp |
| pip | pip install memex-mcp |
| source | git clone github.com/STiFLeR7/memex && uv sync |
For a shared team setup (one Neo4j + one memex-server, auth on by default, Neo4j's ports never exposed to the host):
bash docker/bootstrap-team-env.sh
docker compose -f docker/docker-compose.team.yml up -dSee docker/TEAM-DEPLOY.md for the full flow, capturing the
initial admin key, and the down -v footgun to avoid.
| Property | Value |
|---|---|
| Output | A Neo4j graph populated continuously from your repo |
| Storage | Neo4j via Graphiti. Bitemporal — every edge has created_at and optional expired_at |
| Context | Bounded, ranked, provenance-aware ContextPacket |
| Integrations | Hermes MemoryProvider, MCP resources/tools, Claude Code, Cursor, Codex, Gemini CLI |
| Failure mode | Fail-open; agent execution continues without memex |
| Granularity | Scales from 50 to 5000+ modules via hierarchical Leiden clusters |
| Synthesis | Gemini Flash distills commits into Decision nodes; Pro for grounded synthesis |
| Confidence | Computed at query time. Two-regime decay (validated half-life ~139d, unvalidated stale at 30d) |
| Write governance | Per-node-type ACL, intent-confirmation on agent writes, explicit corroborates / supersedes semantics |
| Goal 10 evidence | 8/8 valid paired runs, 0 treatment failures, 0 treatment regressions |
flowchart TD
Init[memex init<br/>extract baseline] --> Watch[memex watch<br/>daemon + git hooks]
Watch -->|commit| Extract[tree-sitter extract<br/>symbols, imports, lockfile]
Extract --> Synth[Gemini Flash<br/>diff → Decision nodes]
Synth --> Write[Graphiti add_episode<br/>+ post-hoc bitemporal SET]
Write --> Decay[Scheduler<br/>nightly confidence decay]
Decay -->|stale edges| Archive[expired_at = now]
Serve[memex serve<br/>MCP stdio/HTTP] -.->|reads| Write
Agent[AI agent] -->|14 MCP tools| Serve
Serve -->|record_decision / record_problem| Write
Cluster[memex cluster<br/>Leiden over hybrid edges] -.->|every N commits| Write
style Init fill:#e8f4ff,color:#000
style Watch fill:#fff4cf,color:#000
style Synth fill:#ffe0cc,color:#000
style Serve fill:#d4f5d4,color:#00014 tools — eight read, four write, two analytic.
| Tool | When |
|---|---|
get_project_context | Session start. Returns a cluster-level briefing under 1500 tokens regardless of repo size |
get_symbol_context | Before editing a function or class. Returns callers, callees, linked decisions |
get_recent_decisions | Last N days of architectural decisions, optionally module-scoped |
get_open_problems | Active bugs and tech debt, sorted by severity |
search_context | Hybrid search: semantic × keyword × graph traversal × RRF merge |
get_stale_context | Edges whose composite confidence dropped below threshold |
explain_change | Given a commit SHA, cross-references the diff with linked Decision/Problem nodes and asks Gemini Pro for a grounded explanation |
predict_impact | Given a file path, returns a ranked list of modules likely affected based on graph coupling (no LLM call) |
| Tool | When |
|---|---|
record_decision | After making a technical choice. Supports corroborates (reinforce) and supersedes (replace) |
record_problem | When discovering a bug or piece of tech debt |
resolve_problem | When a tracked problem is fixed |
invalidate_edge | When a stored fact is no longer true |
Confidence is not a stored number that mutates. It is computed at query time from base_confidence, validation status, time since last reinforcement, and access count.
flowchart LR
Edge[Edge created<br/>base_confidence] --> Q{Validated by<br/>a human?}
Q -->|yes| Slow[Slow regime<br/>half-life ~139d]
Q -->|no| Fast[Fast regime<br/>stale at exactly 30d]
Slow --> Score[Composite score<br/>conf × recency × rehearsal]
Fast --> Score
Score -->|below floor| Stale[get_stale_context surfaces it]
Score -->|access| Bump[last_reinforced_at updated]
Bump --> Score
style Slow fill:#d4f5d4,color:#000
style Fast fill:#ffd4d4,color:#000| Property | Value |
|---|---|
| Validated half-life | ~139 days |
| Unvalidated stale threshold | 30 days (composite < 0.3) |
| Recency τ | 90 days (exponential decay) |
| Composite formula | conf × recency × (1 + rehearsal_w × log(1 + access_count)) |
| Conflict similarity threshold | 0.4 (below this + overlapping validity = conflict) |
| Intent-confirmation threshold | 0.85 (MCP write similarity check) |
memex cluster runs hierarchical Leiden over a hybrid edge graph:
| Edge type | Weight |
|---|---|
| Directory co-location | 1.0 |
| Module imports | 2.0 |
| Symbol calls | log(1 + calls) |
| Property | Value |
|---|---|
| Algorithm | graspologic.partition.hierarchical_leiden with fixed seed |
| Naming | TF-IDF top-3 over module docstrings + symbol names, parent-dir fallback |
| ID pinning | Jaccard ≥ 0.5 across reruns (cluster names stay stable through renames) |
| User overrides | .memex/clusters.yaml — any assignment can be locked |
| Context budget | get_project_context stays under 1500 tokens whether your repo has 50 or 5000 modules |
memex tracks token reduction metrics and human review actions locally in a SQLite database (~/.config/memex/telemetry.db).
You can query your savings at any time using the CLI:
memex statsOr view the raw JSON payload:
memex stats --jsonOr target a specific repository scope:
memex stats --repo /path/to/repoThis returns an aggregation of:
today, last 7 days, last 30 days, and lifetime.The same statistics are exposed via the HTTP MCP transport:
GET /stats?repo=/path/to/repo
Authorization: Bearer <your-key>Marketplace install above does this for you. Manual wiring in .claude/settings.json:
{
"mcpServers": {
"memex": {
"type": "stdio",
"command": "npx",
"args": ["-y", "stifler-memex-mcp", "serve", "--repo", "."]
}
}
}Add to ~/.cursor/mcp.json:
{
"mcpServers": {
"memex": {
"command": "npx",
"args": ["-y", "stifler-memex-mcp", "serve", "--repo", "."]
}
}
}Add to ~/.gemini/settings.json:
{
"mcpServers": {
"memex": {
"command": "npx",
"args": ["-y", "stifler-memex-mcp", "serve", "--repo", "."]
}
}
}Add to ~/.codex/config.toml:
[mcp_servers.memex]
command = "npx"
args = ["-y", "stifler-memex-mcp", "serve", "--repo", "."]memex can back Claude's native memory tool — agents read from a per-session graph projection plus a writable scratch zone.
memex memory-tool serve --repo . # in-process
memex memory-tool serve --repo . --transport http # FastAPI on :7464from memex.memory_tool import MemexAsyncMemoryTool
memory_tool = MemexAsyncMemoryTool(repo_root=".")
client.beta.messages.run_tools(..., tools=[memory_tool])| # | Principle | The bet |
|---|---|---|
| 1 | Bitemporal, never destructive | Edges are expired, not deleted. WHERE r.expired_at IS NULL filters live state |
| 2 | Confidence is computed, not stored | Mutating a number invites silent drift. Recompute every read |
| 3 | Two regimes for decay | Validated facts decay slowly; unvalidated facts must earn their place by being accessed |
| 4 | Human in the loop | memex review queues lowest-confidence Decision nodes for explicit validation |
| 5 | Write governance | Per-node-type ACL. Decision.policy = open, Module.policy = locked. Intent-confirmation on similar-content writes |
| 6 | Tokens are budgeted | get_project_context stays under 1500 tokens at any repo size via Leiden clusters |
| 7 | Synthesis only on commits | The watcher batches by debounce window. Gemini Flash is not in the hot path of a tool call |
| 8 | Pro for synthesis, Flash for extraction | explain_change uses Pro because grounding matters. Everything else uses Flash |
| 9 | Multi-repo aware | One watcher + one MCP server can manage hundreds of repos. --repo switches scope |
| 10 | Local-first | Neo4j runs in your Docker. Gemini is the only outbound call, and only on commits |
| Use it when | Skip it when |
|---|---|
| Multi-week or multi-month project | One-shot script, throwaway prototype |
| You work across multiple agents (Claude, Cursor, Codex) and want shared context | You only ever pair with one agent on one task |
| Architectural decisions are made over time and need to be remembered | The whole project fits in a single 200k-token context window |
| You want to query "what did we decide about X" from any session | Your repo is already small enough to paste into the prompt |
| Multiple developers using AI agents on the same codebase | Solo work where you never /clear |
memex/
├── memex/
│ ├── extractor/ tree-sitter + lockfile parsers
│ ├── graph/ Neo4j writes, confidence, archive, cluster engine
│ ├── synthesizer/ Gemini Flash → Decision nodes
│ ├── mcp_server/ 14 MCP tools (read + write + analytic)
│ ├── memory_tool/ Anthropic memory_20250818 adapter
│ ├── watcher/ daemon + git hooks
│ └── cli.py init / watch / serve / review / graph / cluster
├── tests/ unit, integration, and objective evaluation suites
├── docker/ Neo4j compose
├── npm/ npx wrapper (publishes as stifler-memex-mcp)
└── Dockerfile introspection-only image for MCP directory sandboxes| Command | What it does |
|---|---|
memex init | Extract baseline graph state, run first cluster pass |
memex watch | Daemon that listens for file + git events and writes to Neo4j |
memex serve | Run the MCP server (stdio, HTTP, or both) |
memex review | TUI that walks lowest-confidence decisions for human validation |
memex graph --output graph.html | Self-contained D3 force layout with cluster overlays |
memex cluster [--rerun] [--dry-run] | Run Leiden over the hybrid edge graph; pin cluster IDs by Jaccard ≥ 0.5 |
memex memory-tool serve | Back Anthropic's memory_20250818 tool with a graph projection |
memex stats [--json] [--repo <path>] | Show context token savings and telemetry stats |
MIT. See LICENSE.
Hill Patel (@STiFLeR7)
Open an issue or PR. uv sync --all-extras installs the development toolchain.
Run uv run pytest -m "not integration" for the offline suite and uv run ruff check . before opening a PR. Version bumps must update pyproject.toml,
npm/package.json, server.json, and the team Docker image tag together.
The v0.9 release record is in CHANGELOG.md, with the
architecture and evaluation evidence under docs/architecture/v0.9/.
Vannevar Bush, 1945: "Consider a future device for individual use, which is a sort of mechanized private file and library. It needs a name, and to coin one at random, memex will do."
Pick your client and paste the snippet. Each one is the same server, written the way that client expects it.
claude mcp add memex -- npx -y stifler-memex-mcp serve --repo .{
"mcpServers": {
"memex": {
"args": [
"-y",
"stifler-memex-mcp",
"serve",
"--repo",
"."
],
"type": "stdio",
"command": "npx"
}
}
}code --add-mcp '{"name":"memex","args":["-y","stifler-memex-mcp","serve","--repo","."],"type":"stdio","command":"npx"}'[mcp_servers.memex]
command = "npx"
args = ["-y", "stifler-memex-mcp", "serve", "--repo", "."]Runs locally on your device. Your client starts the server itself, so nothing has to be hosted.
Paste this prompt into your agent. It reads this page and does the setup for you.
Read https://aiagentslisting.com/mcp/memex to learn what the "Memex" MCP server does and how to install it. Add it to my coding agent's MCP configuration as documented on that page, then confirm the server connects and list the tools it exposes.Agents can also browse this directory over MCP at https://aiagentslisting.com/api/mcp
npx stifler-memex-mcp init --repo .
npx stifler-memex-mcp watch --repo .
npx stifler-memex-mcp serve --repo .This server runs locally, so we can't read its tool list over the web yet.
Paste this line near the top of your repository's README. The badge always renders the current score.
[](https://aiagentslisting.com/mcp/memex)Nothing comparable is listed yet.
v0.9.0memex v0.9.0Release notesv0.8.0-trustv0.8.0 — TrustRelease notesv0.7.0v0.7.0 — NetworkRelease notesv0.5.1Release notesv0.4.0Release notesv0.3.8Release notesv0.3.3Release notesv0.2.0Release notesv0.1.1Release notesConnect to the AI Agents Listing MCP server at https://aiagentslisting.com/api/mcp using the HTTP transport and complete the sign-in when it asks. Then call the submit_review tool for the listing "memex" with a rating from 1 to 5 and a short note on what worked and what did not.One email a week. New agents, MCP servers and skills, and what is actually getting traction.