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graph substrate for coding agents (Claude Code, OpenCode, any MCP-stdio host) — Apply-Gate + on-disk Kuzu store + MCP tools","maintainers":[{"name":"andreassigloch","email":"andreas@siglochconsulting.de"}],"readme":"# GraphCode — governed graph substrate for coding agents\n\n**GraphCode** gives a coding agent (Claude Code, OpenCode, …) a **governed graph** of a project's\nmodel — requirements, tests, modules, traces — behind an **MCP-stdio** surface. The agent **KNOWS**\nthe elements to touch from a precise graph query instead of guessing them with grep. Code stays as\ntext in the repo; the **model lives in the graph**.\n\n## Commands\n\nAll commands run **inside the target repository**:\n\n```bash\nnpx @sigloch/graphcode init          # THE install. One command, one download: scaffolds .mcp.json,\n                                     # GRAPHCODE.md and the store dir; the GVE viewer comes along as a\n                                     # dependency, so the first start needs no network.\n                                     # ↓ everything below is run FOR you or only when you need it ↓\nnpx @sigloch/graphcode mcp           # THE server — your agent host starts this from .mcp.json; you\n                                     # normally never type it. Brings up all three: MCP-stdio, the\n                                     # read-only HTTP/SSE bridge, and the GVE dashboard.\nnpx @sigloch/graphcode status        # is my host up, and where is MY dashboard? Read-only: asks the\n                                     # viewer via api/config WHICH REPO it serves instead of\n                                     # guessing a port. Exit 1 if either is missing.\nnpx @sigloch/graphcode host          # FALLBACK only — the bridge alone, for a repo with no agent\n                                     # session running. Alongside a live `mcp` it hits the store lock.\nnpx @sigloch/graphcode run \"<intent>\" # author the graph via the embedded executor — a local LLM\n                                     # or Anthropic BYOK drives graph_generate/mutate directly, no\n                                     # coding-agent harness. Env: GRAPHCODE_LLM_BASE_URL +\n                                     # GRAPHCODE_LLM_MODEL (required), GRAPHCODE_LLM_BACKEND=\n                                     # openai|anthropic (default openai), GRAPHCODE_LLM_API_KEY.\n                                     # A SIG Local gateway speaks both: backend openai or anthropic,\n                                     # GRAPHCODE_LLM_API_KEY, trust its CA via NODE_EXTRA_CA_CERTS.\n                                     # Stops at handoff, at maxRounds, or when fewer than\n                                     # GRAPHCODE_LLM_SATURATION_MIN_NODES (10) new nodes landed in the\n                                     # last GRAPHCODE_LLM_SATURATION_WINDOW (20) rounds.\nnpx @sigloch/graphcode rewind <ref>  # recall the graph state committed at <ref> — reads the snapshot\n                                     # from git object storage, so the working tree is NOT touched.\n                                     # Aborts while un-exported model edits are pending (--force drops them)\nnpx @sigloch/graphcode upgrade       # install the latest version, refresh artifacts, stop the old host — PRESERVES the store\nnpx @sigloch/graphcode skills sync   # re-copy the shipped se-* skills (overwrites on version mismatch)\nnpx @sigloch/graphcode remove        # remove all scaffolded artifacts (restlos)\n```\n\n## Get started\n\n**Prerequisite:** Node ≥ 22. Nothing is installed globally — graphcode lives per repo, as a\ndependency in its `package.json`.\n\n**Fresh clone of a repo that already uses graphcode?** Skip `init` — `.mcp.json` and\n`GRAPHCODE.md` are committed. Run `npm install` and open the agent host: the store `.graphcode/`\nis gitignored, and the host builds it on first start from the committed model\n(`docs/graph/*.graph.json`, seed-on-empty). Then continue at step 3.\n\n**1. Scaffold** (idempotent, self-contained):\n\n```bash\nnpx @sigloch/graphcode init\n```\n\n| Artifact | Purpose | Commit? |\n|---|---|---|\n| `.mcp.json` | Claude-schema host config — launches `npx @sigloch/graphcode mcp` | ✅ commit |\n| `opencode.json` | the same server in OpenCode's schema (`mcp.graphcode`) | ✅ commit |\n| `.graphcode/` | the per-repo Kuzu store (`.graphcode/kuzu`), created lazily on first run | ❌ gitignore |\n| `GRAPHCODE.md` | guardrails for agents working in the repo | ✅ commit |\n| `GRAPHCODE-STEERING.md` | the human's companion — the four decisions only you can make, and what `docs/views/` is | ✅ commit |\n| `package.json` | gains the `@sigloch/graphcode` dependency | ✅ commit |\n\nBoth host configs are written every time and **merged**, never overwritten: a foreign MCP server\nin `.mcp.json`, or your `provider` / `model` block in `opencode.json`, survives `init`, `update`\nand `remove` — only the `graphcode` entry is ours.\n\n**2. Add `.graphcode/` to `.gitignore` and reload your agent host.** Claude Code picks up\n`.mcp.json`, OpenCode picks up `opencode.json`. The agent then sees a `graphcode` MCP server\nexposing the tools below.\n\nThe MCP surface is the agent-agnostic contract — any MCP-stdio host works. The `se-*` **skills**\nare Claude Code surface (`.claude/skills/`); an OpenCode user drives the same tools directly.\n\n**3. Say this to your agent.** That is the whole first step — the server prints the same line on\nstartup:\n\n> Lies GRAPHCODE.md, dann: `graph_readiness` — wo steht das Projekt und was ist der nächste Schritt?\n\nOn an empty repo (no model yet) start from the intent instead:\n\n> Lies GRAPHCODE.md, dann leg mit `se:generate` los: \"&lt;was das System tun soll, in einem Satz&gt;\"\n\n**4. Dashboard — already running.** `graphcode mcp` starts the GVE viewer itself, along with the\nread-only `/health` + `/events` (SSE) bridge. Do **not** start a second server — ask where yours is:\n\n```bash\nnpx @sigloch/graphcode status\ngraphcode status — auth-service  (/Users/you/dev/auth-service)\n  MCP-Host    OK             pid 40001, seit 2026-08-19T09:12:03.000Z\n  Dashboard   OK             http://localhost:4318/\n```\n\n`status` reads `docs/views/dashboard.url` (GVE writes its actual bound address there on startup,\nremoves it on shutdown) and then asks that instance `api/config` **which repo it serves**. The\naddress itself is stable per repo — GVE derives it from the repo path (43000–43999) — so your\nbookmark keeps working across restarts; the identity check stays as the safety net for the rare\ncollision, where Vite bumps and a neighbour's viewer could end up on the address yours left behind.\nOnly an instance serving THIS repo is reported as yours. Opt out with `GRAPHCODE_NO_GVE=1`; the bridge port comes from `GRAPHCODE_HOST_PORT` in\n`.mcp.json` `env`, which `init`/`update` scaffolds per repo.\n\n**Lifecycle — the host lives exactly as long as your session (CR-GC-370..372).** Closing the\neditor (or anything that ends the stdio client) shuts the host down in order: viewer → HTTP\nbridge → `host.sock` → store lock. Reopening therefore wins a REAL election instead of proxying a\nhost whose editor is gone, and brings its dashboard back at the same address. Three guards behind\nthat: a viewer that dies mid-session is restarted (1 s / 3 s / 10 s, then it says so and stops\ntrying); the store lock carries a heartbeat, so a lock without a pulse for 90 s is free even if its\nPID is alive (PID reuse after a reboot, a hung host); and a host whose lock was taken over notices\nat its next beat and ends its session rather than becoming a second writer.\n\n**5. To upgrade:** run `graphcode upgrade` — one command: installs the latest version, lets THAT build refresh `.mcp.json`,\n`GRAPHCODE.md` and skills, never touches the store.\n\n## Using it — the agent loop (over MCP)\n\nThe agent drives the whole loop through MCP tools — every write goes through the **one Apply-Gate**\n(`mutate()`): rule-checked, author-logged, blocked on new violations.\n\n1. **Spec** — `graph_mutate` adds requirements/tests/modules + traces through the gate. A REQ with no\n   verifying TEST (or unresolved by a MOD) is **rejected** — drift can't land.\n2. **KNOW, not grep** — `graph_impact(id)` returns the *exact* blast-radius (the incoming dependents:\n   the tests and modules that touch the changed node) as a bounded Format-E slice, never a full dump.\n   `graph_expand` deepens one branch on demand.\n3. **Implement** — `graph_mutate` updates node status as code lands; the change persists to disk Kuzu.\n4. **Re-export** — `graph_export` serializes the live graph to commit-able docs: canonical\n   `docs/graph/<member>.graph.json` (the SSOT) + deterministic `docs/views/*.md` (GENERATED headers).\n   This is the single sync path — never hand-edit the graph JSON.\n\nThe member name (`<member>.graph.json`) is derived from the repo's `package.json` name (unscoped),\nfalling back to the repo directory name.\n\n### MCP tools\n\nAll 23 MCP tools, grouped by role — this table is complete, and a test asserts the count against the\nlive registry so it cannot silently fall behind the code.\n\n| Role | Tool | What it does |\n|---|---|---|\n| **read** | `graph_elements` | filtered slice of the graph, never a full dump |\n| | `graph_get_node` | one node with its attributes |\n| | `graph_get_edges` | the traces of one node |\n| | `graph_impact` | the exact blast-radius: who breaks if I change this (KNOW, not grep) |\n| | `graph_expand` | deepen one branch on demand |\n| | `graph_context` | the definition-of-done pack for ONE node — spec closure in one call |\n| **write** | `graph_mutate` | the write path — through the Apply-Gate (human or AI, same gate); also binds model to code: `~ FUNC-x` + `@realRef {…}`, `@testRefs [...]` on a TEST |\n| | `graph_merge` | replay a branch worktree's command log onto this store (semantic rebase); the node merge is Format-E `M source + target` via `graph_mutate` |\n| | `graph_reseed` | in-process reseed from the committed SSOT, with an automatic backup |\n| **measure** | `rules_evaluate`, `rules_get_violations` | run the SE rules read-only |\n| | `graph_readiness` | the readiness report: dimensions, phase gates, blocking errors |\n| | `graph_metrics` | per-module architecture metrics **plus the thresholds they were judged against** |\n| **generate** | `graph_generate` | the cold-start driver: seed → expand → handoff, as a state machine |\n| | `graph_suggest` | rank candidate fixes by how far they move the graph toward your target |\n| | `graph_authoring_guide` | the legal edges for a given element type, before you write |\n| **test evidence** | `graph_test_ingest` | feed a test run's results back into the graph |\n| | `graph_test_report` | the report over those results |\n| | `graph_tests` | which tests exist, and what they are bound to |\n| **export** | `graph_export` | re-export the live graph to `docs/graph` + `docs/views` |\n| **audit** | `audit_trail`, `audit_stats` | mutation history — every gate write logged |\n| **help** | `graph_help` | explain any rule ID, gate, or dashboard token (read-only) |\n\nThe `realRef`/`testRefs` binding and `graph_test_ingest`/`graph_test_report`/`graph_tests` are the answer to the obvious\nobjection that a model can drift from its code: the binding is an attribute the rules check (R-19,\nR-20), and \"done\" means a test result landed in the graph, not that someone ticked a box.\n\n### Bringing an existing project in\n\nYou do not have to start from an empty graph. Two import paths ship, with **deliberately different\nsemantics** — the difference is safety-relevant, not cosmetic:\n\n| Skill | Source | Semantics |\n|---|---|---|\n| `se:import-code` | an existing TypeScript codebase | deterministic extraction via graphify — **no LLM**. Produces FUNC/MOD/FLOW/SCHEMA, never use cases or requirements (nobody can read intent out of code). **RESEED, not merge**: the graph is replaced, and a backup is written automatically first. |\n| `se:import-doc` | a document (PDF / Markdown / text) | two-stage: the skeleton is shown to you, you decide the element types in chat, then an LLM extract goes through the Apply-Gate like any other write. **MERGE (adds only)** — nothing existing is removed. |\n\nUse `import-code` to bootstrap a brownfield repo's architecture layer, then `import-doc` to bring the\nspecification in on top of it.\n\n### Generated documents\n\nThe SE document family is rendered from the graph, deterministically — same graph, same bytes. Each\nhas a skill that renders it into `docs/views/`:\n\n| Skill | Document |\n|---|---|\n| `se-view:rtm` | Requirements Traceability Matrix |\n| `se-view:arch` | Architecture allocation (SDD) |\n| `se-view:icd` | Interface Control Document |\n| `se-view:nfr` | NFR register |\n| `se-view:testconcept` · `se-view:testmatrix` | test concept (pyramid + computed E2E gap) · VCRM |\n| `se-view:intplan` · `se-view:implplan` | integration & test plan · implementation plan (MS/CR) |\n| `se-view:conops` | Concept of Operations (ISO 29148 §5.2.4) |\n| `se-view:fmea` | FMEA — failure modes, S/O/D, action priority |\n| `se-view:trade` | trade studies — decisions and superseded options |\n| `se-view:changelog` | change log from the CR history |\n\nBecause they are generated, \"the document is incomplete\" and \"the gate is still open\" are the same\nfact with the same cause — there is no separate documentation debt to track.\n\n`se-retro` computes the six KPIs over a finished stretch of work (graph-vs-grep, tool usage,\ntoken/LOC, plan conformance, gate health, binding coverage).\n\n### Help — explain any item, for both audiences\n\nEvery on-screen token is explained in three layers (plain · in SE terms · the exact fix),\nfor a systems engineer who doesn't know this encoding **and** a user with no SE background:\n\n- **`se:help <token>`** — explain a rule (`R-04`), gate (`CDR`), panel, or artifact (`fmea`).\n- **`se:help`** (no argument) — ranked, explained next steps from the live readiness + violations.\n- **`graph_help`** — the read-only MCP tool the skill is a thin surface over.\n\nThe plain/SE wording is authored once (`src/surface/help-content.ts`); titles, severity, and the\nowning gate are derived from `V3_RULES` + readiness, so help never drifts from the live model.\n\n## What it is / is not\n\n- **IS:** Bridge + Store + MCP tools + Apply-Gate. Agent-agnostic, headless, one Kuzu store per repo.\n- **IS NOT:** a generator (→ aimprove), a learning engine (→ learning-core), a viewer/dashboard, or an extractor (→ graphify).\n\n## Viewer integration\n\nGraphCode is headless and is **not** itself a viewer — it ships the read-only **data layer**, and\n`graph-view-edit` (GVE) is the renderer that consumes it. The elected host **spawns GVE for you**\n(see *Get started* step 4); these are the pieces it wires up:\n\n- the read-only HTTP/SSE bridge — owns the single Kuzu store and serves `/health` + `/events`.\n  No mutating HTTP verb is reachable; the write path stays MCP-stdio.\n- panel shapers (`readinessPanel`, `impactPanel`, `artifactsPanel`, …) — pure read-only\n  view-models over the MCP tools; the renderer consumes these and fills the render mount-slot.\n- live-update events — every gate mutation emits one update event the host broadcasts over SSE.\n\nThe bound address is announced in `docs/views/dashboard.url`, never a fixed port. The shared view\ncatalog (which documents exist, under which filename) lives in `@sigloch/graphcode-client` so the\nviewer can list them without depending on the exporter.\n\n## Local development (this repo)\n\n```bash\nnpm install        # everything from the registry — no private repo needed\nnpm run build      # tsc → dist/\nnpm test           # vitest — real disk Kuzu, no mocks\n```\n\nThe five `@sigloch/*` dependencies (`contracts`, `graph-api-core`, `graph-cypher-wasm`,\n`learning-core`, `se-steering`) are published packages, so a clone builds and tests without any\nsibling checkout. To work against a local checkout of those packages instead, run\n`npm run link:siblings` (`npm link`, reversible with `npm install`).\n\n### Migrating a graph across the REQ-kinds major (contracts 10.x)\n\ncontracts 10.x narrows `REQ.kinds` to exactly one of `functional | non-functional`, moves\n`risk`/`mitigation` to `attributes.role`, drops `precondition`/`postcondition`, and lets a FCHAIN\nsatisfy only `non-functional`. An old graph still boots; R-18 flags the affected `satisfy` edges.\n`scripts/migrate-req-kinds.mjs` (CR-GC-669) moves it in two steps:\n\n```bash\nnode scripts/migrate-req-kinds.mjs propose --repo <repo> [--graph <name>] --out decisions.json\n# review: every entry with decidedBy \"heuristic\" or \"open\" is a per-REQ decision — edit kinds/\n# role/dropSatisfy/addSatisfy, then set decidedBy to your name\nnode scripts/migrate-req-kinds.mjs apply --repo <repo> [--graph <name>] --decisions decisions.json\n```\n\n`apply` writes one batch through `graph_mutate` and exports via `graph_export` — no hand edit. It\nrefuses unconfirmed heuristic entries (`--accept-heuristic` only for trial runs on copies) and a\ndecision file that no longer matches the graph. It opens the repo's store itself, so stop the\nrepo's MCP host first.\n\n## Constraints (locked)\n\n- **One store = Kuzu**, embedded, single-writer, on disk (`.graphcode/kuzu`) — never `:memory:`.\n- **One transport = MCP-stdio** — no Express/REST in the core.\n- **One Apply-Gate = `mutate()`** — every edit (human or AI) goes through it; the author is only logged.\n- **SE ontology + `V3_RULES` from `@sigloch/contracts/se`** — imported, never forked. A new\n  ElementType/TraceType/rule requires a family review + version bump.\n\n## Model & docs\n\nGraphCode owns the **implementation** plus its own graph model. The graph SSOT for graphcode's\nown model is [`docs/graph/graphcode.graph.json`](docs/graph/graphcode.graph.json); the claims,\ndefinition of done and test status are in [`docs/graphcode_leitlinie.md`](docs/graphcode_leitlinie.md) (German).\n[`docs/articles/`](docs/articles/) is the plain-language introduction; the numbers it cites come\nfrom [`docs/spikes/`](docs/spikes/) (raw benchmark runs, reproducible via [`rig/dummy-slicer/`](rig/dummy-slicer/)).\nGraphCode is part of a larger internal toolchain; some design-history documents reference private\ngovernance docs that are not part of this repository.\n\n## License\n\nMIT — see [LICENSE](LICENSE).\n","readmeFilename":"README.md"}