MCP Assist — Coordination Memory

mcp-assist-memory

A generic, project-agnostic memory / coordination / artifact server for multi-agent and multi-surface work. One FastAPI process serves a 30-tool MCP over Streamable HTTP, backed by Postgres (+ pgvector), deployed standalone on a Replit Reserved VM.

This is Tier 1 of the reusability contract: every project reuses it as-is. It carries zero domain terms — project identity lives in namespace values, never in tool names, tables, columns, or code.

Capabilities at a glance

• 30-tool MCP over Streamable HTTP (memory, handoff, session, artifact, coordination, feedback, admin).
• Trust-boundary spine (Plan v2) — actor-scoped exactly-once writes with visible dedup, read-back-verified acks (verified_persisted), standardized error payloads with remedies, write-time screening + quarantine, provenance tiers (origin, model attribution, derived_from lineage), trust decay (needs_reverification), PHI-safe tool_events telemetry, per-namespace variant profiles, and an observation_log feedback channel.
• Namespace-scoped multi-tenancy — every per-project query filters on namespace.
• Resilient to transient DB drops — the server transparently retries genuine connection losses (Neon scale-down / PgBouncer recycle, SQLSTATE 57P01/08xxx) on a fresh pooled connection, and validates connections at checkout, so callers no longer have to retry. Retries are idempotency-gated, so they never double-write.
• Prompt-injection resistance layer — values are sanitized on write (forged markers are escaped one-way to [[UNTRUSTED_DATA]], never reconstructed on read), instruction-shaped writes are screened and quarantined (visible in the write ack; include_quarantined: true opts reads back in), and reads come back wrapped in <<<UNTRUSTED_DATA>>> markers; storage.sanitize.unwrap_value recovers the raw value when a consumer needs it (e.g. to json.loads). Honest framing: these are layers, not proofs — deterministic screens and wrappers are bypassable by an adaptive attacker; adversarial evaluation is pending (see Phase 10 backlog in DECISION-PROTOCOL.md).
• Content-addressed artifacts (sha256, global dedup), 50 MB cap, ranged reads.
• Per-surface rotatable tokens (web vs. desktop-cli) managed from a password-gated /admin dashboard.

The 30 tools

Sequences are the paths an agent should take. Correct use of this server has always been a sequence — learn which database answered, resolve the profile, check what is stale, then act — and that ordering used to live in tool descriptions and skills, i.e. it was enforced by a model remembering advice mid-task, and a skipped step produced no signal whatsoever. The three sequence tools run their steps server-side in a fixed order and return steps_run, so the ordering is something the server did rather than something a caller got right. They are strictly additive: every primitive they are built from still works exactly as before, for surgical use.

recall and memory_search now share ONE retrieval guard (storage/retrieval.py): the same absolute floor and relative alpha the Intent Gate applies. Previously memory_search had no floor at all while intent_open had both, so the same store answered the same question differently depending on which tool the caller reached for. They still differ in what they do with the verdict — memory_search annotates every row and drops nothing, recall filters by default and reports the rejected counts — but they can no longer disagree about what counts as a match.

The Intent Gate (claude/intent-gate/INTENT_GATE_CHARTER.md) is a per-namespace opt-in (variant_profiles.profile.intent_gate: "on"): mutating tools gain a deterministic Tier-0 pre-flight (two-phase preview/confirm for supersession + delete, dependency-freshness flags, compact gate ack block), intent_open adds the Tier-1 memory-similarity critic, and Tier 2 (LLM reasoning over the direct Anthropic API — never MCP sampling) ships behind tier2: "on" (default off). Default-profile namespaces are byte-identical to the pre-gate server.

/healthz (liveness) and the /admin token dashboard are served separately (not MCP tools).

Tenancy — namespace is the project boundary

namespace == project == tenant. One namespace per project (e.g. acme-billing), with conventional sub-scopes by key prefix (coord/…, knowledge/…). Every per-project tool takes a required namespace and every query filters on it — there are no implicit cross-project reads. The session and session_event tables carry namespace too, so episodic memory is scoped like everything else.

Artifacts are the deliberate exception: they are content-addressed (sha256) and dedup globally, so they are not tenant-scoped — the hash is the capability.

Honest limit (and the v2 fix)

The per-surface tokens scope which client surface connects, not which project it may touch: any holder of any active token can pass any namespace, so namespace remains a soft boundary — real isolation for honest clients, not enforced against a misbehaving one.

v2 auth roadmap — per-project tokens/roles. A token scoped to acme-billing must not be able to read or write other-project. Until then, treat the namespace boundary as a convention enforced by client configuration, not by the server. (See REUSABILITY.md → "namespace is the tenant boundary".)

Auth & the /admin dashboard

MCP tokens are stored in Postgres (admin_auth_tokens) and rotatable from /admin without a redeploy. There is one active token per surface:

The gate accepts any active token, so each surface can be rotated or revoked independently — rotating web never disturbs desktop-cli or cursor. The /admin page shows one card per surface with a ready-to-paste URL/command and its own rotate button.

MCP_AUTH_TOKEN seeds the web token on initial boot (so an existing claude.ai connector keeps working); desktop-cli and cursor are auto-generated. After first boot the dashboard is the source of truth.

• /admin is password-gated by ADMIN_PASSWORD (signed, HttpOnly session cookie, CSRF-protected). Without it the dashboard refuses logins.
• The only routes not behind the bearer gate are GET /healthz, the streamed GET /artifact/{sha256}, and /admin (which self-authenticates).

Stateless transport. /mcp runs in stateless HTTP mode (http_app(stateless_http=True)): every request is self-contained, with no in-memory session affinity. Client sessions therefore survive VM restarts/redeploys, and the three surfaces share no server-side session state.

Architecture

• One AsyncConnectionPool created in the FastAPI lifespan (app.py), injected via deps. Nothing else opens a connection. The pool is built with check=AsyncConnectionPool.check_connection, so a connection terminated server-side while idle is validated and discarded on checkout, never handed to a caller.
• One config.py (pydantic-settings) — the only place secrets are read.
• StorageBackend ABC (storage/base.py) implemented by PostgresBackend; the 18 tools map 1:1 onto it.
• Transparent reconnect: reads and idempotent writes retry on a connection drop (_retry_on_disconnect), so e.g. OperationalError: terminating connection due to administrator command (SQLSTATE 57P01, Neon scale-down / PgBouncer) is retried on a fresh pooled connection instead of surfacing to the caller. Only genuine disconnects (08xxx / 57P0x / an already-closed connection) are retried — other operational errors (lock timeout, too-many-connections) surface unchanged. Writes retry only when a replay is safe: artifact_put (content-addressed) always, and memory_save/handoff_save/memory_delete only when given an event_id (exactly-once). The session_* writes also retry, with an explicit tradeoff: a drop in the narrow commit-ack window means session_create may orphan an empty, unreferenced session row, and session_append_event is at-least-once (a replay can append one duplicate event). For an append-only session log that beats failing the call outright; a save with no event_id still runs once and surfaces the error.
• Write-path sanitize strips forged delimiters/control chars; reads wrap values in <<<UNTRUSTED_DATA>>> markers (lethal-trifecta defense). Note: the value (and session-event payload) fields come back wrapped, so a consumer that needs the raw value — e.g. to json.loads a value that was a JSON string — must strip the markers first. Use storage.sanitize.unwrap_value (or strip_untrusted for a single string); the wrapping stays applied on every read.
• Bounded lifespan readiness (no unbounded pool.wait()), 50 MB artifact cap, ranged blob reads, idempotent event_id writes, idempotent blob backfill.
• Semantic recall (memory_search): when a VOYAGE_API_KEY is set, every memory_save embeds the entry (Voyage, voyage-3.5-lite, 1024-dim) into a nullable embedding vector(1024) column with an HNSW cosine index, and memory_search ranks live entries by meaning (embedding <=> query), then backfills keyword/substring matches up to limit. Embedding is best-effort: it runs before a connection is taken and never blocks (or fails) a write, and with no key the column stays NULL and search degrades to pure keyword — the pre-Phase-3 behavior. Every leg filters on namespace first (no cross-project recall). After enabling a key on an existing DB, embed old rows once with python scripts/backfill_embeddings.py (idempotent, only touches NULL rows).
• Recall tuning (hnsw.ef_search): the HNSW index is approximate, so a larger store can miss relevant hits unless its query-time recall parameter is tuned. memory_search sets hnsw.ef_search per-statement (transaction-local, semantic leg only) from HNSW_EF_SEARCH (default 100; pgvector's own default is 40). Higher = better recall, slightly slower search; it must be >= the search limit to take effect. Small stores return the same rows regardless, so the default is safe to leave alone — raise it (e.g. 200) if a large tenant reports missing results, lower it toward 40 to shave latency. Very large tenants can also tune the index build parameters (m, ef_construction); see migrations/0002_embeddings.sql (changing those requires recreating the index).
• Coordination reconciler (coord_reconcile): when GitHub access is available, a claim (with meta.repo + meta.pr/meta.branch) is resolved against live GitHub — is PR #N merged? what is branch X's head? — and stamped with an append-only verdict; without access it stays unverifiable (never a wrong current). Access is sourced in priority order: an explicit GITHUB_TOKEN (read-only repo + PRs), else — on Replit — the connected GitHub account via the Replit connector (token fetched fresh per cache-window so it survives OAuth refresh), else disabled. Resolution is best-effort: a network/API failure yields unverifiable, never a blocked write. GITHUB_WEBHOOK_SECRET enables POST /webhook/github to reconcile affected claims on push / pull_request.
• Memory curator (coord_curate): when ANTHROPIC_API_KEY is set, a finished session can be consolidated write-side: coord_curate(namespace, session_id) reads the session's execution trace plus similar existing memories, asks the model what is worth persisting, and applies the resulting ADD/UPDATE/MERGE/SUPERSEDE/NOOP operations deterministically. Every op passes a fail-closed PHI gate first, claims without provenance (meta.repo + meta.pr/branch) are downgraded to notes, supersession sets a validity boundary (history is kept, never deleted), and writes are idempotent (deterministic event_id) so re-running a session never double-writes. It is best-effort: without the key the curator is disabled and coord_curate is a clean no-op ({curator_enabled: false, operations: []}), and any model/parse failure yields zero operations — never a wrong write. dry_run=True returns the proposed operations without writing. CURATOR_MODEL and CURATOR_MAX_OUTPUT_TOKENS tune it. Curated rows also carry a second hyde_embedding, so memory_search can match a future question (HyDE leg) as well as the stored statement.

Run locally

cp .env.example .env          # DATABASE_URL + MCP_AUTH_TOKEN + ADMIN_PASSWORDmake install                  # pip install -c constraints.txt -e ".[test]"make migrate                  # apply migrations/0001_init.sqlmake run                      # uvicorn app:appcurl localhost:8000/healthz   # {"status":"ok","db":"ok"}# token: open http://localhost:8000/admin and sign in with ADMIN_PASSWORD

Tests (real Postgres)

The suite runs against a real Postgres and skips cleanly if DATABASE_URL is unset. The neutral test project is proj-test (never a real project name).

DATABASE_URL=... make test

CI (.github/workflows/test.yml) spins an ephemeral Neon branch per run, migrates it, runs pytest, and deletes the branch. Set repo secrets NEON_API_KEY and NEON_PROJECT_ID to enable it.

Smoke test (the connector handshake)

scripts/smoke_mcp.py performs the exact handshake a Claude connector does — initialize + tools/list over /mcp with a valid token — and asserts HTTP 200 with the full 30-tool surface, plus the guard rails (no/bad token ⇒ 401, /healthz db ok). It exists so a transport/auth/host regression (like the fastmcp 3.4.3 421) can never ship silently again.

• Blocks a bad build: the in-process half runs in CI via pytest (tests/test_smoke_mcp.py) against the ephemeral Neon branch — a broken handshake, gate, or tool count fails the build before it can deploy.

• Flags an unhealthy live deploy: run it against the deployed URL after a deploy. It exits non-zero on any failed check:

  bash

  SMOKE_BASE_URL=https://<your-vm> SMOKE_TOKEN=<active token> make smoke

  .github/workflows/smoke.yml runs this against a live URL on manual dispatch (or a 6-hour schedule); set repo secrets SMOKE_BASE_URL and SMOKE_TOKEN to enable it (it no-ops cleanly when unset).

Deploy on Replit (Reserved VM)

1. In Secrets, set DATABASE_URL (pooled endpoint), MCP_AUTH_TOKEN, and ADMIN_PASSWORD (plus optional Phase-3 keys).
2. Deploy as a Reserved VM (deploymentTarget = "vm") — not Autoscale; the durability gate needs the process to persist.
3. The deploy run step runs python scripts/migrate.py then starts uvicorn.
4. Open https://<your-vm>/admin, sign in, and copy/rotate the token. Point each client at https://<your-vm>/mcp.

Pinned dependencies (deterministic builds)

pyproject.toml declares loose ranges, but the deploy build, post-merge.sh, and make install all pass -c constraints.txt, so prod installs the exact versions verified in dev. This is the guardrail against the class of failure that caused the prod /mcp 421 outage (an unpinned build silently resolving a newer fastmcp).

To intentionally upgrade a dependency (so pins don't rot):

pip install -U <pkg>          # or `pip install -e .` to re-resolve a widened rangemake test                     # AND exercise /mcp locallymake lock                     # regenerate constraints.txt from the verified env# then redeploy — prod now installs the newly verified set

Never hand-edit versions in constraints.txt; always regenerate with make lock (scripts/lock-deps.sh). The file header documents the same procedure.

Postgres / Neon

Use the pooled connection string for the running service; psycopg is configured with prepare_threshold=None for PgBouncer transaction pooling. Tests and scripts/migrate.py use a direct endpoint (the test pool keeps prepared statements on).

Boundary

This repo is Tier 1 only. Canvas-specific MCP tools, FHIR logic, and SDK knowledge live in the separate canvas-sdk-tools repo — never here.

Blob migration (filesystem → bytea)

python scripts/backfill_artifacts.py /path/to/old/blobstore

Idempotent (dedup by sha256), streams each file, skips/reports anything over the 50 MB cap, and verifies a random sample by checksum readback.