mushroomdb

The graph that stays true — and knows who's allowed to see it.

mushroomdb is the data layer for agents that reason over entities. It is an embedded Rust graph database in which a relationship is a schema declaration: write a rule once, and every write derives, maintains and retracts the matching edges, each one carrying the rule, the score and the values that produced it. An agent reaches it over MCP — fifteen tools on an entity store — or you embed it as a Rust library, a Python module, or a sidecar beside your own service. Four questions are what it exists for: why are these two related (explain_association, answered with the evidence rather than an assertion), what did that look like then (edges_at, the edges a node had at any past commit), what would this change do (what_if, computed without writing anything), and who may see it (query with a role, so one graph answers differently per caller). Local-first: a directory on disk, no account, no endpoint, no model call in the write path unless you enable embeddings.

ingest-git stays supported as a data source: commits, pull requests, files and authors become entities with rule-derived relationships, which is what makes a ticket↔commit link a rule rather than a script.

Deprecated in 0.6.4: the code-graph door — the explore, map, context, impact, owners, why and sync tools, the three grep/edit hooks, and the plugin's coding-assistant positioning. It still works and is still tested; it is removed in 0.7. See Deprecations.

Pre-1.0 alpha — APIs and formats may change between minor versions.

Docs · Changelog · Issues

A single SET changes one property; the rule fires, new scored edges are derived and the stale ones retracted, inside the same write

Quick start

npx mushroomdb install --db ./memory

One command writes the /mushroom skill, an MCP server listing the fifteen-tool association surface, and the session hooks. Then a worked flow, four tool calls:

upsert_entity  →  create_rule  →  find_similar  →  explain_association
  (store)           (link)           (recall)          (explain)

Full tool reference: docs/site/mcp.md.

Live, not a snapshot. One SET on a property re-derives the matching edges — added, scored and retracted — before the write closes. The SET in the GIF above is that one write.
Retracts instead of going stale. A property drifting out of a rule's predicate doesn't leave a stale edge behind; the engine retracts it in the same write that caused the drift.
Explains any link. explain_association names the rule, the score, and the values the two entities actually share, so "why are these two related?" has an answer your assistant can quote instead of a guess.
Knows who's allowed to see it. Pass a role or a mask with a query and the same graph answers differently per caller; write statements are rejected on masked queries.
Answers what it said last week. edges_at returns the edges a node had at a past commit; mushroomdb asof ./db --commit 5 --query "…" replays the WAL to that commit, derived edges included.

Where it fits

What it is

An embedded, single-binary graph database with a rule engine that maintains edges for you.
A 27-tool MCP server — fifteen listed on an entity store, three on a store built by ingest-git — plus a /mushroom skill and a Claude Code plugin.
Safe for several processes at once: one writer at a time behind an advisory LOCK file, any number of readers, and every handle picks up a peer's commits by refresh() rather than reopening — so a running serve, an editor hook, a git hook and a CLI command can share one store. docs/site/concurrency.md
Local-first: your data stays on disk, no cloud service, no model call in the write path unless you enable embeddings.

What it isn't

Not a hosted memory service — there is no account, no endpoint, nothing to sign up for.
Not a vector database. Vector predicates and HNSW are built in; bring your own embeddings.
Not a Postgres replacement. Single writer, no interactive transactions, memory-first storage.

Deprecations

What "deprecated" means here. It still works in 0.6.4, it is still tested on every release, and nothing is removed. It is no longer promoted — not on this page, not in the skill's task rules, not in the plugin's description — its documentation page opens with a notice, and an install that turns one of the hooks on prints a deprecation line. It is removed in 0.7. The migration is nothing to do, unless you relied on the specific thing named below.

Deprecated	If you relied on it
The tools `explore`, `map`, `context`, `impact`, `owners`, `why`, `sync`	Pin `mushroomdb@0.6.x`. Nothing on the entity surface replaces them: they answer from a repository graph, which 0.7 stops shipping tools for. `ingest-git` and `query` keep answering the same facts as Cypher.
The hooks `--intercept-grep`, `--impact-before-edit`, `--enrich-grep`	Re-run `install` without the flag; the hook comes out the way any other manifest entry does. Nothing replaces them.
The plugin's coding-assistant positioning	The plugin is not going away. Its description and skill now lead with entity memory.
Code-suite benchmark runs	`python3 benchmarks/agent-tasks/run.py --suite code` still runs. No further runs are committed; the committed summaries stay as the record.

Why, measured. Across 240 cells — arms stock / installed / invoked / cli × 3 reps × 20 tasks over two repositories — the invoked graph arm scored 0.924 against stock's 0.927 (paired difference -0.0035 [-0.0112, 0.0017]) and cost $0.2713 against $0.2267 (+0.04463 [+0.01312, +0.07471], about +20%), and the two installed-but-not-invoked arms made 0 graph calls in 120 sessions: results/20260910T000418Z. An agent holding grep neither needs a graph for those questions nor chooses one. What the engine is for is measured separately, on the association suite, and reported under Benchmarks.

The differentiator

Most graph databases require you to create edges manually or run a batch similarity script after each load. mushroomdb makes edge creation a schema declaration. A rule like "connect every Person to every Org whose skills list overlaps theirs by at least 50%" is written once:

db.create_rule(RuleDef {
    name: "skill_fit".into(),
    src_label: "Person".into(),
    dst_label: "Org".into(),
    predicate: Predicate::Overlap { field: "skills".into(), min: 0.5 },
    edge_type: "FIT".into(),
    weight_prop: Some("score".into()),
    max_edges: Some(5), // keep the 5 best-matching Orgs per Person (top-k per source)
}).expect("rule");

After that, every insert_node and set_prop evaluates the rule incrementally. The engine writes the edge, stores the Jaccard score, and retracts the edge if the properties later diverge — without any manual work.

Watch it live — a Cypher SET changes one property, the founded_within rule fires, and new scored edges appear in the bundled explorer:

A SET statement deriving new scored edges live

Open the Rules panel, and the Why slide-over shows the exact predicate arithmetic behind every derived edge:

Rules panel and Why slide-over showing overlap arithmetic

Predicates

Six predicate kinds ship today. They compose via All(...) (AND, score = min) and Any(...) (OR, score = max), nested up to depth 4.

Predicate	What it tests
`KeyMatch`	FK equality — source field matches destination key
`FieldEqual`	Exact match on a named scalar field (string, int, float, bool)
`Overlap`	Jaccard on list-valued fields, min threshold
`NumericWithin`	Absolute numeric difference within a tolerance; score = `1 -
`GeoRadius`	Haversine distance on `[lat, lon]` fields within km; score = `1 - dist/radius`
`VectorSimilar`	Cosine similarity on float arrays, min threshold

Auto-FK: fields ending in _id whose values match existing node keys get KeyMatch rules created automatically at ingest time. VectorSimilar accepts approximate: true to switch candidate selection to in-tree HNSW (per-query recall min 0.90, mean 0.998 at 5k nodes / dim 1536, fixed-seed probe). Full reference: docs/site/rules.md.

Built on the same engine

Live subscriptions. subscribe_rule (Rust) and GET /subscribe (WebSocket) stream EdgeFired / EdgeRetracted the moment they hit the WAL — not polled, not batched. Bounded 65,536-event queue; slow consumers get a Lagged { missed: N } marker instead of a disconnect. docs/site/subscriptions.md
Rule attribution across time. Every derived edge writes a HISTORY-MARKER WAL record carrying the rule name, so edge_history, node_history, and was_linked answer which rule created a link and at which commit. GraphDb::open_at(&dir, 5) replays to a past commit, derived edges included; out-of-range commits return CommitOutOfRange, never wrong data. docs/site/timetravel.md
Materialized views. Degree counts and neighbor aggregates (sum/avg/min/max) maintained incrementally on every edge change — no cron, no triggers, no stale caches. docs/site/views.md
Rule suggestions. db.suggest_rules() (or mushroomdb suggest ./db) profiles your data and ranks candidate rules with estimated edge counts and rationale. Seeded sampling, so the same database always returns the same suggestions. No rule is ever applied automatically. docs/site/suggest.md

Agent memory

Graph structure captures the shape of real knowledge — entities, associations, similarity, and lineage — and rule-derived edges keep those associations fresh as new facts arrive.

Entities map to nodes (Person, Document, Project, Concept, …).
Associations are edges derived from data: cosine similarity on embeddings, shared field values, FK relationships, geographic proximity. Declare a rule once; every write maintains the matching edges without agent-side bookkeeping.
Recall has three modes: find_similar by query vector (HNSW when available, brute force otherwise); find_similar by key (neighbors along a rule-derived edge type); query for structured Cypher recall. hybrid_search fuses fulltext and vector results via Reciprocal Rank Fusion.
Explanations are built in: explain_association shows which rules and scores produced each link, so an agent can cite evidence instead of asserting a conclusion.
Node masks are the ACL primitive: pass mask: [key1, key2, …] to query to restrict the visible node set. Write statements are rejected on masked queries. docs/site/masks.md
Schema-as-code: mushroomdb schema apply <dir> <schema.json> idempotently applies rules, views, and fulltext indexes, printing a created/updated/unchanged diff.

Minimal workflow (four tool calls):

upsert_entity  →  create_rule  →  find_similar  →  explain_association
  (store)           (link)           (recall)          (explain)

Fourteen task tools answer a question in prose in one call. Seven answer on any store; seven are the deprecated code door. They are what the skill reaches for, and what tools/list shows first:

Tool	Purpose
`explore`	Deprecated (0.7). One tool to find: `context`, `impact`, `history` or `all` for one target in one reply, capped by a token `budget`
`map`	Deprecated (0.7). The repository in one screen: size, last sync, clusters, key files, owners, hot files
`context`	Deprecated (0.7). One file or symbol from every side: where it is as `path:start-end`, signature, callers, callees, importers, co-change partners, commits, notes. `full` adds the body
`impact`	Deprecated (0.7). What changing these files reaches: partners with scores, importers, symbols other files call, owner. Defaults to the working tree's diff
`owners`	Deprecated (0.7). Top author and share, who else knows the file, last touch, the split by quarter
`why`	Deprecated (0.7). Every rule edge between two nodes with its evidence, or the shortest path when there is none
`explain_association`	Why two entities are associated: every rule-derived edge between them, with the rule, the score, the predicate it matched, and the values the two actually share
`node_edges`	Every edge on one node, grouped by edge type, with the rule and score behind each. `all_of: [types]` answers with the partners linked by every one of them, as keys; `edge_type`, `label`, `direction` and `limit` narrow it further
`neighborhood`	At depth 1 the same grouped listing; above 1 the breadth-first `(key, label, depth)` table
`edges_at`	The edges a node had at one 0-based WAL commit — the graph as it was, not as it is — with the same `all_of` / `edge_type` / `label` / `direction` filters
`what_if`	The derived edges a property change would lose and gain, computed without writing anything. `edge_type` prints both sides as partner keys
`recall`	One pointer per hit — `path:line symbol — first doc line` — for the identifiers in a topic
`remember`	Write a note into the graph and return its key
`sync`	Deprecated (0.7). Bring the store up to date: commits since the last sync, then the dirty working tree

Each of the fourteen also takes json: true, which answers with the raw report instead of the rendered digest.

The thirteen graph tools reach the store directly. Their descriptions are prefixed Advanced: in tools/list, so an assistant knows which surface is the front door. The default listing follows the store: a store built by ingest-git lists three tools in all — explore, query and stats — and any other store lists fifteen, the association surface: query (with an optional role), explain_association, neighborhood, node_info, node_edges, was_linked, edges_at, what_if, node_history, edge_history, find_similar, hybrid_search, remember, recall and stats. All 27 stay served either way — the listing decides what a session can call, not what the server answers — and mushroomdb mcp <db> --all-tools lists the whole set:

Tool	Purpose
`upsert_entity`	Insert or update a node by key (no existence check needed)
`ingest_json`	Batch-ingest nodes of one label from a JSON array
`create_rule`	Declare a derivation rule; backfills existing nodes immediately
`find_similar`	Find similar nodes by query vector (HNSW) or by derived edge traversal
`hybrid_search`	RRF over fulltext + vector results
`explain`	The rules and scores that link two nodes, as JSON — `explain_association` above answers the same question in prose
`query`	Cypher query (read or write); pass `mask` for an ACL-scoped read, or `role` to answer as one role from the store's `roles.json`
`node_info`	Return a node's key, label, and properties
`stats`	Live node, edge, and rule counts
`node_history`	WAL change history for a node (archives included; a `snapshot --truncate` ends the reach)
`edge_history`	Add/retract lifecycle for edges between two nodes, with rule attribution
`was_linked`	Point-in-time edge check: was an edge active at a given commit?
`rename_node`	Rename a node's key; old_key, new_key

Full walkthrough, tool reference, and Claude Desktop setup: docs/site/mcp.md. Skill, plugin, and hook details: docs/site/skill.md.

Install options

claude plugin install mushroom@mushroomdb   # after `claude marketplace add MatthewSherlin/mushroomdb`
npx mushroomdb install            # skill + MCP server + hooks, no toolchain needed
cargo install mushroomdb-cli      # `mushroomdb` binary from crates.io (no embedded UI)
cargo add mushroomdb              # embedded Rust library
pip install mushroomdb            # Python bindings

install writes an MCP entry that runs npx -y mushroomdb@<version>, so the assistant needs nothing installed globally and nothing is copied into your home directory. Point it at a local build with --command <path>. mushroomdb doctor verifies the result end to end — config entry, store, lock, hooks, git hooks, and a real stdio handshake with the configured command.

To see the bundled explorer, write a demo graph and serve it:

mushroomdb demo ./db
mushroomdb serve ./db

Open http://127.0.0.1:8080/. The demo graph has 10 Orgs, 20 Projects, 30 People, and 334 edges — 304 of them derived by seven rule sets. When a token is configured, open http://host:8080/?token=…. Building the binary with the UI embedded, Docker, and the install.sh script are covered in CONTRIBUTING.md.

Role-bound tokens limit a caller to a named subset of nodes. Define roles in schema.json under the roles key (each role has a label selector list), then pass --role-token TOKEN:ROLE (repeatable) when starting the server, or set MUSHROOMDB_ROLE_TOKENS="tok1:role1,tok2:role2". A role token receives only the nodes matching its label selectors — read endpoints return rows filtered to the visible set; write, subscription, and analytics endpoints return 403. Unknown token or role name: 401. The never-widen invariant is enforced in the server: a client-supplied mask is always intersected with the role mask. The MCP interface (mushroomdb mcp) is a stdio JSON-RPC server for local agent use and is not subject to bearer-token or role enforcement.

CLI reference

Command	What it does
`mushroomdb install [--platform claude-code\|cursor\|codex\|all] [--project\|--user] [--db <path>] [--command <path>] [--delivery cli\|mcp\|both] [--no-git-hooks] [--intercept-grep] [--impact-before-edit] [--enrich-grep] [--always-load\|--no-always-load] [--no-prewarm]`	Write the `/mushroom` skill + MCP server entry + the `SessionStart`, `UserPromptSubmit` and `PostToolUse` hooks + git hooks. Auto-detects platform and scope. `--delivery cli` writes no server entry: the skill teaches the binary instead. The three experimental hooks — grep redirect, blast radius before an edit, symbol facts after a search — are off by default; `alwaysLoad` on the server entry is on by default for an install that pins a store with `--db`
`mushroomdb uninstall [--platform …] [--project] [--db <path>]`	Remove exactly what `install` wrote (manifest-driven; leaves user files)
`mushroomdb disable [--platform …] [--project\|--user]`	Turn an install off without removing it: strips the MCP entry, the hooks and the git hook blocks. The skill, the store and `.gitignore` stay
`mushroomdb enable [--platform …] [--project\|--user]`	Turn a disabled install back on, re-resolving the command instead of replaying what `disable` removed
`mushroomdb doctor [--project\|--user] [--platform …]`	Verify an install: config entry, npx reachability, store, lock, hooks, git hooks, a real stdio handshake, and duplicate-scope servers. Exit 1 on any `fail`
`mushroomdb ingest-git <dir> <repo> [--exclude <pattern>]... [--prs] [--no-structure] [--no-docs] [--ensure-gitignore]`	Graph a git repository: `Author`, `Commit`, `File`, `Symbol` nodes plus `CO_CHANGED`, `KNOWS`, `IMPORTS`, `CALLS` and `MENTIONS` rules. Re-run to sync. See `docs/site/ingest-git.md`
`mushroomdb brief <dir>\|--auto`	The repository's shape from the graph alone — counts, last sync, most central files, most called symbols — capped at 4,000 bytes and byte-stable between runs. Hook body for `SessionStart`
`mushroomdb explore <dir> <target> [--depth context\|impact\|history\|all] [--full]`	Deprecated (0.7). One tool to find: `context`, `impact` and `owners` composed behind one depth
`mushroomdb map <dir> [--json]`	Deprecated (0.7). The repository in one screen: clusters, key files, owners, hot files, and three questions worth asking
`mushroomdb context <dir> <target> [--full]`	Deprecated (0.7). One file or symbol from every side. `<target>` is a path, a symbol key, or a bare symbol name. The body is quoted only with `--full`
`mushroomdb impact <dir> <file>...`	Deprecated (0.7). What changing these files reaches: co-change partners, importers, and the symbols other files call
`mushroomdb owners <dir> <path>`	Deprecated (0.7). Top author and share, who else knows it, last touch, the last four quarters
`mushroomdb why <dir> <a> <b>`	Deprecated (0.7). Every rule edge between two nodes with its evidence, or the shortest path between them
`mushroomdb sync <dir>\|--auto [--json]`	Deprecated (0.7). Re-sync the repository the store was built from: new commits, then the working tree where it differs from `HEAD`. Takes no repo argument — reads it off the graph. `--json` prints the counts as one object. The git hooks `install` writes use `--auto`, so each worktree syncs its own store
`mushroomdb touch <dir>\|--auto [<file>...]`	Re-extract just these files. With no `<file>` reads them from a `PostToolUse` payload on stdin (hook body)
`mushroomdb recall <dir>\|--auto`	Hook body for the `/mushroom` skill's `UserPromptSubmit` recall hook: reads a prompt payload on stdin, prints one pointer per hit for the identifiers the prompt names, and nothing when it names none. Wired automatically by `install`
`mushroomdb intercept <dir>\|--auto`	Hook body for the optional `PreToolUse` grep redirect (`install --intercept-grep`): reads a `Grep` payload on stdin and exits 2 with a pointer at `explore` when the pattern is a symbol the graph holds
`mushroomdb mcp <dir>\|--auto`	Start a stdio MCP JSON-RPC server for agent tools
`mushroomdb demo <dir>`	Write a deterministic demo graph (10 Orgs, 20 Projects, 30 People)
`mushroomdb serve <dir>`	Start the HTTP server + optional UI (default `127.0.0.1:8080`; `--token` on non-loopback; `--role-token TOKEN:ROLE`)
`mushroomdb query <dir> <cypher>`	Run a Cypher read or write (`--query` also accepted)
`mushroomdb asof <dir> --commit N`	Read-only view at a WAL commit
`mushroomdb stats <dir>`	Print node/edge/rule counts
`mushroomdb suggest <dir>`	Rank candidate linking rules (scored top-k 32, KeyMatch 512)
`mushroomdb schema apply <dir> <schema.json>`	Idempotently apply a schema file (rules, views, fulltext indexes); prints a diff
`mushroomdb snapshot <dir> [--keep-wal\|--truncate] [--retention N]`	Write `snapshot.bin` and archive the WAL as `wal.<N>.archive`, so history reads still reach it. `--truncate` discards it; `--keep-wal` leaves `wal.bin` whole
`mushroomdb verify <dir>`	Audit snapshot integrity: CRC32 all 12 sections, exit 2 on any mismatch
`mushroomdb migrate <dir>`	Migrate an older store format in place
`mushroomdb backup <dir> <dest>`	Copy store files to `<dest>` and CRC-verify the copy. WARNING: unsafe against a running `serve` — use `POST /backup` for live-served stores
`mushroomdb export <dir> <dest> [--format jsonl\|parquet\|graphml]`	Export nodes, edges, and rules. JSONL is byte-identical across runs; Parquet is not across library versions. GraphML exports nodes and edges only, as a single `.graphml` file, for import into generic graph viewers and analysis tools
`mushroomdb algo pagerank\|wcc\|degree <dir> [--top N]`	PageRank, weakly-connected components, or degree centrality over manual + derived edges. `--weight-prop`/`--min-weight` weight or filter the edge set
`mushroomdb algo communities <dir> [--edge-type T]... [--weight-prop P] [--min-weight X] [--top N]`	Louvain communities with per-community cohesion and overall modularity
`mushroomdb --version`	Print the CLI's version and exit

Concurrency: every CLI write command, the hooks, and a running mushroomdb serve coordinate through one advisory LOCK file in the store directory, so they are safe to run against the same store at the same time. A writer that cannot get the lock within two seconds exits 3 with another mushroomdb process is writing; retry, having written nothing. Readers never take the lock and never wait; recall opens read-only (read_only: true) so an unattended hook can never delay a writer or fail because one is running. What the lock does not give you: cross-process transactions, and subscription events for a peer's writes — a commit absorbed by refresh() is visible on the next read but notifies nobody. Full model: docs/site/concurrency.md.

Full HTTP endpoint reference: docs/site/api.md.

Known limitations

Limitation	Detail
Memory-first	The in-memory store is RAM-bound. Design target is 10M nodes (~5–15 GB with properties). mmap-backed storage is deferred.
Single writer, no interactive transactions	One writer at a time, many readers — within a process via `RwLock`, across processes via the advisory `LOCK` file. `write_batch` commits all ops in one WAL frame (all-or-nothing on crash replay) but is not isolated: readers may observe intermediate states while a committed batch is applied in memory. Multi-statement `BEGIN`/`COMMIT` is not supported, and there are no cross-process transactions.
Peer writes do not notify subscribers	Commits another process made are picked up by `refresh()` and are there on the next read, but they fire no `EdgeFired`/`EdgeRetracted` event, so `/watch` and `/subscribe` see only writes made through this process. Poll if you need to react to a hook's writes.
Cold start without a snapshot re-fires all rules	Snapshots persist derived edges, ANN state, and view definitions. At 100k nodes / ~10M derived edges: 0.02 s from a V8 snapshot vs 8.16 min WAL-only (ANN re-fit dominates). Call `snapshot()` before close. See `dogfood/results/scale-100k.md`.
Two-hop Cypher joins at scale	Dense patterns producing >1,000,000 intermediate rows error without `LIMIT`. Add `LIMIT n` — the pull-based executor stops early and never materializes the full binding table.
Cypher write subset	CREATE, MATCH…SET, MATCH…DELETE, MATCH…DETACH DELETE, and MERGE (single-key, with `ON CREATE SET` / `ON MATCH SET`) are supported. Derived edges cannot be deleted manually. Variable-length paths are hard-capped at 10 hops; unbounded `*min..` is rejected at parse time. Full coverage table: `docs/site/query.md`.
Approximate vector mode is opt-in	`approximate: true` enables HNSW candidate selection. Per-query recall min 0.90, mean 0.998 at 5k / dim 1536 (fixed-seed probe). Review the trade-off before using it in completeness-critical workloads.
Demo refuses existing directories	`mushroomdb demo` exits 1 if the target directory is non-empty, including hidden files (`.DS_Store` counts). Use a fresh path.
Python bindings return dicts	pandas/polars zero-copy is not wired yet. HTTP `POST /query` defaults to Arrow IPC; JSON via `?format=json`.

Benchmarks

10,000-node graph (Apple M4 Pro, macOS 15.7.3, arm64), mushroomdb v0.1.1 release build, 2026-08-24. Full methodology and honesty notes: benchmarks/results/head-to-head-10k-v2.md.

Workload	mushroomdb	Neo4j	KùzuDB	Memgraph
Bulk ingest	784 ms	13.2 s	1.21 min	12.5 s
Neighborhood depth-1 (p50)	0.4 µs	1.22 ms	99.6 µs	1.34 ms
Neighborhood depth-1 (p95)	2.2 µs	1.46 ms	519 µs	2.14 ms
Neighborhood depth-2 (p50)	0.2 µs	7.18 ms	1.08 ms	9.22 ms
Cypher scan-filter-project (1.4k rows)	1.22 ms	93.7 ms	3.95 ms	83.7 ms
Cypher two-hop join (200 rows)	261.6 µs ★	3.99 ms ★	1.59 ms ★	1.96 ms ★
Cold-start: V8 snapshot open	0.02 s ▽	—	—	—
Cold-start: WAL-only open	8.16 min ▽	—	—	—
Server boot-to-ready	n/a (embedded)	6.6 s	n/a (embedded)	4.3 s

Honesty notes:

mushroomdb numbers are embedded — no network round-trip, no serialization overhead. KùzuDB is also embedded, so its numbers are directly comparable. Neo4j and Memgraph go over bolt/localhost (~0.1–1 ms round-trip per query).
★ Two-hop join: same dataset, same warmup policy, all four engines on 5,810,000 INDUSTRY_ALIGNMENT edges. Fresh process → ingest + preload → 3 discarded warmups → median of 10 runs. mushroomdb derives the edges via create_rule; competitors were pre-loaded via UNWIND MERGE or COPY FROM CSV. All engines return 200 rows.
★ Earlier v2.1 two-hop values were retracted for cross-engine contamination; the v2 mushroomdb 307 µs figure was retired (measured on a smaller 1M-edge graph). Both are documented in the methodology file rather than quietly dropped.
▽ 100k cold-start measured 2026-08-28, warm file cache, cold process, /usr/bin/time -l: V8 snapshot open 0.02 s at 31–41 MiB RSS; snapshot size 1.8 GiB; snapshot write ~35 s. Cold-cache was not measured. See dogfood/results/scale-100k.md.
Rule engine vs hand-rolled maintenance (10k nodes, 1,000 specialty updates, drift = 0 for all three): per-op expert-written 64.93 min, batched expert-written 24.98 s, rule engine 17.58 s. Both hand-rolled variants were written by the engine team with full knowledge of retraction semantics — drift = 0 is a property of that, not of hand-rolling in general. benchmarks/results/handrolled-vs-rules.md

Agent benchmarks measure the entity engine directly. benchmarks/agent-tasks/ runs real claude -p sessions against executable truth. The association suite (--suite association) asks twenty relationship questions of one generated world written three ways — as JSON files, as a single relational file, and as a mushroomdb store. The graph arm moved from 0.795 at $0.5089 (20260911T005749Z) to 0.967 at $0.0923 (20260911T065400Z) against the relational baseline's 0.974 at $0.1158 — a correctness tie at a lower mean cost, and still behind files + grep (1.000 at $0.0949) on a 2,000-entity world; the gate failed on the cost interval. The code suite (--suite code) is retired; its committed summaries stay as the record. docs/site/association-bench.md describes the suite and how to rebuild the world.

Architecture

graph-db/
├── crates/
│   ├── core-storage      # Packed adjacency topology + columnar property store + WAL + snapshots
│   ├── core-rules        # linking rules, per-rule indexes, incremental maintenance
│   ├── core-query        # pull-based interpreter; traversal ops + Cypher subset
│   ├── core-api          # the one public Rust interface; typed error enums
│   ├── code-extract      # tree-sitter symbol/import/call extraction; bytes in, facts out
│   ├── arrow-bridge      # results ↔ Arrow buffers
│   ├── server            # axum HTTP + WebSocket; serves UI
│   ├── cli               # mushroomdb binary
│   └── sim-harness       # DST: virtual clock, fault-injecting IO, seeded runner
├── ui/                   # TypeScript + Vite graph explorer
├── bindings/python/      # PyO3 / maturin
└── clients/typescript/   # HTTP + WebSocket client

Dependency rule (inward only): bindings/server/cli → core-api → {core-query, core-rules} → core-storage

Storage uses a dense-id WAL with per-commit fsync (configurable via FsyncPolicy), plus mmap-able V8 rkyv snapshots (12 sections: CSR topology, columnar properties, HNSW blobs, provenance, IVF state, per-node last-change index, and more — zero-copy, no heap allocation on open). V5/V6/V7 stores are auto-migrated to V8 on GraphDb::open. Derived edges are not WAL-logged; they are restored directly from the mmap'd sections. See docs/format-stability.md for the format evolution contract.

Roadmap

Phases 1–4 and Plan 18 all landed. What remains:

Priority	Item
Medium	mmap snapshots; lock-free epoch readers
Medium	v1.0 format stability (snapshot + WAL semver guarantee)
Low	`CASE` in a write-statement `RETURN`; subqueries; napi-rs; WASM
Low	Multi-statement `BEGIN/COMMIT` interactive transactions

Docs

Quickstart · Rules · Cypher reference · HTTP + MCP API
The live code graph (deprecated in 0.6.4, removed in 0.7) · Concurrency · Codebase graph
Install, plugin and hooks · MCP tools · Association benchmark
Time travel · Subscriptions · Views · Rule suggestions
Masks and access control · Full-text search · Property indexes · Graph algorithms
Durability and recovery · Panic policy · Testing · Format stability
Design spec · Moat roadmap · Case study

Building from source, Docker, packaging, and the test gates are in CONTRIBUTING.md.

License

Dual-licensed under MIT or Apache-2.0, at your option.

mushroomdb 0.6.4