# Synaptic Code Intelligence [Health: Active] **Category:** 🧠 Knowledge & Memory **Repository:** https://github.com/ColinVaughn/Synaptic **GitHub Stars:** 23 **Views:** 0 **Installs:** 0 **Upvotes:** 0 **Directory Page:** https://allmcps.com/mcp/synaptic-code-intelligence ## Description Code intelligence for repository graphs, change impact, test selection, and engineering memory. ## Claude Desktop Quick Installation Remote MCP endpoint (confidence: high). Install path detected from listing signals. Add as a URL/SSE server in your client: ```json "mcpServers": { "synaptic-code-intelligence": { "url": "https://discord.gg/ytX7R2PbNz" } } ``` ## Documentation & README # Synaptic

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Synaptic is a source-grounded code maintenance platform built around three connected systems: **API maintenance**, **repository memory**, and a persistent **knowledge graph**. Together they let an engineer or AI assistant understand what the code does, remember what has happened to it, and make bounded repairs without guessing. 1. **API maintenance** keeps external dependencies and SDKs safe to change. Dependency bots can tell you a new version exists; Synaptic inventories the APIs your code actually uses, detects source-grounded breaking changes, finds the affected call sites, plans a bounded repair in an isolated worktree, verifies graph invariants and selected tests, and only publishes a draft PR when the evidence is complete. 2. **Repository memory** preserves the history that usually lives in people, chats, failed branches, incident notes, and old PRs. It records previous changes, regressions, decisions, procedures, verification results, and external artifacts as source-linked evidence, then retrieves that memory through the CLI or MCP server so future work starts with context instead of archaeology. 3. **The knowledge graph** is the structural map underneath everything. Synaptic turns any folder, monorepo, or federated set of repositories into a persistent, queryable graph of symbols, files, resources, calls, imports, inheritance, SQL usage, dynamic-dispatch hazards, and cross-repo edges across 30+ languages with [tree-sitter](https://tree-sitter.github.io/). The graph answers architectural questions, traces reverse impact ("what would this change break?"), forecasts and speculatively runs changes before you make them, plans safe refactors, diffs architecture across git history, and audits SQL for performance and security. Memory adds what the graph cannot infer from the current tree alone. API maintenance uses both to turn upstream change into evidence-backed repair plans. It all ships as a single static Rust binary (`synaptic`) with no runtime and no interpreter, writes machine-readable graphs alongside human-readable reports and 2D/3D/SVG visualizations, and exposes an MCP server so an AI coding assistant can use these systems before grepping or reading files. If you do not want to run the MCP server yourself, **Synaptic Cloud** is a paid hosted MCP service for using Synaptic with your projects: [synapticgraph.com](https://synapticgraph.com/). For commit-triggered graph sync and verified API or dependency draft repairs, follow the [GitHub automation guide](https://synapticgraph.com/docs/github-automation). ## Use Synaptic with a project Start from any repository root. Synaptic writes its index and reports to `synaptic-out/` and keeps project-specific configuration under `.synaptic/`. The easiest path is to ask your AI coding agent to install and configure Synaptic for the current repository, then have it follow the [Installation](https://github.com/ColinVaughn/Synaptic/wiki/Installation), [Quickstart](https://github.com/ColinVaughn/Synaptic/wiki/Quickstart), and [Assistant Integration](https://github.com/ColinVaughn/Synaptic/wiki/Assistant-Integration) guides. If you prefer to do it yourself, the manual path is: ```sh # 1. Install the binary from this repository cargo install --path bin/synaptic # Or download a prebuilt binary from GitHub Releases, then confirm it works synaptic --version # 2. Build the first graph for your project cd path/to/your/project synaptic extract . # 3. Ask structural questions without rereading the whole codebase synaptic query "authentication flow" synaptic affected parse_config synaptic search --pattern god-class # 4. Keep the graph current as the project changes synaptic update synaptic watch synaptic hook install ``` For a normal project setup, add a `.synapticignore` if there are generated, vendored, or sensitive paths you do not want indexed; `extract` also honors `.gitignore` and skips common secrets like `.env` and key files. Use `synaptic hook install` when you want Git commits, checkouts, and graph merges to keep `synaptic-out/graph.json` fresh automatically. Once the graph exists, turn on the higher-level systems as needed: ```sh # Repository memory: ingest history, docs, decisions, and outcomes synaptic memory refresh --root . synaptic memory search "previous auth migration" # API maintenance: configure monitored APIs and check real usage synaptic api init synaptic api discover --json synaptic api coverage --json synaptic api scan --offline --json # AI assistant integration: serve the graph and memory over MCP synaptic serve synaptic install codex --global ``` The safest mental model: run `extract` first, use `query` / `affected` / `search` to explore, add hooks or `watch` when the project is active, then enable `memory` and `api` workflows when you want Synaptic to preserve history or maintain external contracts. --- ## Why - **Structural clarity.** God nodes, surprising cross-module connections, import cycles, and community structure are computed for you. - **Impact and foresight.** Reverse impact, change forecasting, and speculative test runs answer "what depends on this?" and "what would this change break?" before you touch the code. - **Token economy.** Querying a compact graph costs a fraction of feeding raw files to an LLM, so an assistant can answer those questions without loading the repo. - **Confidence you can audit.** Every inferred relationship is tagged `EXTRACTED`, `INFERRED`, or `AMBIGUOUS`. - **Scales past one repo.** A workspace can federate many repos with real cross-repo edge resolution (export surfaces plus import / tsconfig / module-federation aliases). - **Offline by default.** A code-only corpus never makes a network call. The optional semantic pass over docs and papers is the only feature that needs an API key. ## Highlights - **30+ languages** via tree-sitter, each built and tested in isolation in CI, plus regex-based extractors for a few formats and script extraction for Vue/Svelte/Astro and Razor/Blazor. See [Languages](https://github.com/ColinVaughn/Synaptic/wiki/Languages). - **One command to a full graph** plus 2D, 3D, and SVG visualizations, a Markdown report, and GraphML / Cypher / DOT / Obsidian / wiki exports. See [Output Formats](https://github.com/ColinVaughn/Synaptic/wiki/Output-Formats). - **Graph queries**: relevant-subgraph search, shortest path, node explanation, reverse-impact ("what depends on this"), find-all-references (`synaptic references` / the `find_references` tool: everywhere a symbol is used, including the imports and inheritance a caller-only view misses), and per-file symbol outlines. See [Querying](https://github.com/ColinVaughn/Synaptic/wiki/Querying). - **Dynamic-dispatch awareness**: event buses (Node EventEmitter, DOM CustomEvent, C# events) and Electron IPC link a publisher to its subscriber through a channel node, so a handler reached only across the bus is not a phantom 0-caller. Reflection and dynamic dispatch that cannot be resolved statically (by-name lookups, dispatch tables, `eval`, dynamic import, .NET/Python/JVM reflection) are cataloged so a "0 dependents" answer is never mistaken for "safe to change": `synaptic hazards` (and the `dynamic_hazards` MCP tool) list the sites, and `affected` attaches a caveat when a symbol is reachable only dynamically. - **Time-travel diff**: `synaptic diff [rev2]` (or `--since `) reports how the graph changed between two git revisions, added/removed dependencies, removed APIs, architectural drift, new cycles, and hotspots, with a Markdown or self-contained HTML report. - **Architectural search (SYNQL)**: `synaptic search` runs a small Cypher-inspired query language over the graph, matching on structure (kind, visibility, LOC, fan-in/out, variable-length paths) with `count(...)` aggregation, `--explain`, saved queries, and a library of named patterns (singleton, factory, observer, service-locator, god-class). Not text search. `synaptic search --file ` lists every symbol defined in a file, ordered by line, with no query needed. - **Safe refactor**: `synaptic refactor rename` / `move` / `extract` emit a confidence-scored execution plan (`plan.json` + `plan.md`) for an AI agent to apply, then `refactor verify` rebuilds and checks the graph held (the definition moved/renamed, no references lost, no new cycles). Synaptic never edits source itself. - **Change forecasting and speculative execution**: `synaptic predict` forecasts a change's blast radius, public APIs at risk, at-risk tests, new cycles, risk score, and a verify checklist before you edit (`--edit ":"` forecasts a described edit before any code is written); `synaptic speculate` then applies the change in a throwaway git worktree and actually runs the at-risk tests plus a build/type-check, reporting real pass/fail — the ground-truth half of prediction; and `synaptic eval replay` replays history to score forecast quality against git ground truth (co-edited tests, removed APIs), turning prediction accuracy into a CI-gateable metric. See [Commands](https://github.com/ColinVaughn/Synaptic/wiki/Commands). - **SQL performance & security audit**: `synaptic sql audit` flags row-level-security gaps, over-broad grants, likely SQL injection, missing indexes on filter/foreign-key columns, `SELECT *`, non-sargable predicates, N+1 patterns, and missing primary keys over the SQL-aware graph (extraction now models columns, indexes, RLS policies, and grants, and links application queries to the tables they touch). `synaptic sql advise --query ""` critiques a candidate query before you write it, cross-referenced against the graph's tables/indexes/RLS. See [SQL Auditing](https://github.com/ColinVaughn/Synaptic/wiki/SQL-Auditing). - **Resource graph** (universal, on by default): data/resource files (data JSON and `.mcmeta` under `assets/`, `data/`, and generated dirs) are indexed as graph nodes, and reference-like strings inside them bind to the file, resource (by path-derived id like `ns:path`), or code symbol they name — so `affected` and `query_graph` span code *and* resources. A generated resource that duplicates a hand-authored one at the same logical path gets a `shadows` edge (surfaced by `readiness_audit`). Framework-agnostic — a Minecraft `ResourceLocation` is just one instance of the logical-id shape. Localization JSON also contributes a bounded set of key-only search aliases (never translated prose), so message catalogs are discoverable without one graph node per translation. `extract --no-resources` restores the code-only graph. - **Port/readiness audit**: `synaptic audit readiness` ranks likely port blockers from graph, source, and config signals: framework sentinel returns, placeholders/stubs, generated-resource noise, and project metadata. The MCP `readiness_audit` tool exposes the same structured report. - **MCP server** (stateless protocol 2026-07-28 with legacy compatibility through 2025-11-25) exposing 30 core tools, five vulnerability tools, and five read-only repository-memory tools over stdio or HTTP: subgraph search, source reading, reverse-impact, find-all-references, dynamic-dispatch hazards, PR/working-tree blast radius, change forecasting, predictive test selection, edit-impact prediction, structural search, time-travel diff, plan-only rename, and SQL audit/advise, plus prompts, completions, resource subscriptions, and structured tool output. See [MCP Server](https://github.com/ColinVaughn/Synaptic/wiki/MCP-Server). - **Source-grounded repository memory**: a temporal overlay for previous changes, failed attempts, regressions, decisions, procedures, verification, external issue/PR/CI/incident artifacts, semantic community summaries, and revision-aware file/symbol lineage. Git hooks capture exact commits and refresh knowledge; principal policy, compact/federated stores, checksummed team bundles, retrieval benchmarks, and aggregate impact evidence are built into the CLI and MCP surface. See [Repository Memory](https://github.com/ColinVaughn/Synaptic/wiki/Repository-Memory). - **Self-maintaining API workflows**: `synaptic api` inventories SDK versions, discovers contracts, records coverage gaps, detects source-grounded breaking changes, localizes affected call sites, and prepares bounded repairs in an isolated worktree. Verification fails closed on incomplete evidence, and only the explicit `publish` stage can create or update an idempotent draft PR. See [API maintenance](https://github.com/ColinVaughn/Synaptic/blob/HEAD/docs/procedures/api-maintenance.md). - **Dependency vulnerability management**: `synaptic vuln` reads every lockfile in a repository across 12 package ecosystems, matches resolved versions against an OSV corpus, and decides whether each advisory actually applies here rather than stopping at a version match. Findings carry an evidence ladder, a dependency path, a CVSS-derived priority, graph-backed call sites and entry-point exposure, and a remediation plan; applicable findings with a fixed target can become bounded, isolated repairs whose patched dependency resolution and repository tests must pass before Synaptic can create one deterministic draft GitHub PR or GitLab MR. Checksummed export/import keeps repair and provider credentials separated, and Synaptic never approves or merges. Accepted risks are time-boxed and expire on their own. Five MCP tools let assistants check packages, run a graph-backed scan, inspect exposure evidence, and request a bounded repair hand-off. Whole-repository scans stay local by default; an agent must opt in before the dependency list is sent to OSV. See [Vulnerability Management](https://github.com/ColinVaughn/Synaptic/wiki/Vulnerability-Management). - **Incremental rebuilds**, file watching, and git hooks keep the graph current. See [Incremental Updates](https://github.com/ColinVaughn/Synaptic/wiki/Incremental-Updates). - **Graph-aware PR dashboard** with blast radius and merge-order conflict detection. See [PR Dashboard](https://github.com/ColinVaughn/Synaptic/wiki/PR-Dashboard). --- ## Token economy A core payoff of querying a compact graph is **reading a small answer instead of the whole codebase**. `query_graph` defaults to a terse, ranked list of the most relevant symbols (a few hundred tokens); pass `full=true` for the whole subgraph with its edges. The figures below measure a *full* subgraph response (at a 2,000-token budget) on Synaptic's own source (199 Rust files, 56,408 lines, **510,966** `cl100k` tokens) -- one such answer to a structural question is **~1,950 tokens**, versus reading the source files it actually touches: A Synaptic query uses about 31x fewer tokens than reading the source files it points to: roughly 1,950 versus 60,900 Across six questions spanning different subsystems, querying the graph used **27-38x fewer tokens** (about **31x overall**) than reading the files the answer references: | Question | Query response | Read the files | Fewer tokens | |---|--:|--:|--:| | http request handling | 1,804 | 48,803 | 27x | | session create / reap | 1,974 | 65,578 | 33x | | query_graph subgraph | 2,011 | 53,759 | 27x | | extraction walker | 1,977 | 70,443 | 36x | | PR fetch / rank | 1,926 | 73,231 | 38x | | incremental merge | 2,010 | 53,440 | 27x | A query response stays small no matter how big the repo gets (it is capped by the token budget), so the ratio grows with the codebase. Note the `graph.json` index itself is large because it encodes every symbol and edge; you never load it into context, you query it and get back only the slice above. **Reproducible.** Tokens are exact `cl100k_base` counts via `cargo run -p synaptic-server --example tokcount`. The baseline is the unique source files referenced by the result (whole files, the conservative grep-then-read case; it does not count the dead-end files you would open without the graph). Run `synaptic extract .` on any repo and compare for yourself. This is a context-compression measurement, not an end-to-end agent-savings claim; the paired SWE-bench/BEIR methodology is in [BENCHMARKS.md](https://github.com/ColinVaughn/Synaptic/blob/HEAD/BENCHMARKS.md#agent-token-efficiency-and-standard-retrieval). ## Advanced-tool performance The analysis tools answer in milliseconds because they run over the in-memory graph, not the source. Criterion micro-benchmarks (dev machine; run `cargo bench -p synaptic-synql -p synaptic-refactor`): | Operation | Workload | Time | |---|---|--:| | SYNQL property query (`search`) | `WHERE`/`loc`/`fan_out` over a 2,000-node graph | **~0.47 ms** | | SYNQL relationship-pattern join (`search`) | one-hop join over a 2,000-node graph | **~0.97 ms** | | Safe-refactor rename plan (`refactor rename`) | hot symbol, ~120 call sites across 40 files, incl. the textual scan | **~4.9 ms** | The 0.6.3 graph-pipeline audit added dedicated Criterion coverage for construction, incremental comparison, and federation (`cargo bench -p synaptic-graph -p synaptic-incremental -p synaptic-workspace`). On the audit fixtures, one-pass 16 x 500-node federation measured **136.1 -> 6.07 ms**, a 10k-node topology comparison **54.92 -> 9.77 ms**, and a 1,000-site duplicate edge **240.74 -> 0.56 ms**. These are machine-dependent micro-benchmarks; the committed fixtures and growth curves are the reproducible evidence. Time-travel `diff` is build-bound rather than query-bound: the graph delta itself is near-instant, and the cost is building each revision in a throwaway git worktree. Built graphs are cached per commit SHA under `synaptic-out/history/`, so a repeat diff of the same commits returns immediately and only the working-tree side is rebuilt. ## Accuracy The token study above is a smoke test on one repo. The relationships Synaptic extracts are validated separately, against a **hand-labeled corpus** of mini-repos whose true call edges, test linkages, blast radii (including distractor nodes that must *not* be flagged), and cross-language couplings (including look-alikes that must *not* connect) are written out by hand in a `ground_truth.toml`. A preflight fails the run if any labeled symbol does not resolve, so a dropped node becomes a loud failure rather than a quietly smaller denominator. Every number below is exact set-comparison against those labels, reproducible with `synaptic eval corpus`: | Fixture | Family | Call P/R/F1 | Aff-test rec | Blast rec / excl / size | Cross P/R/F1 | |---|---|---|---|---|---| | systems-rust | systems-rust | 100/50/66 | — | 100% / 100% / 1.0 | — | | scripting-python | scripting-python | 100/100/100 | 100% | 100% / 100% / 2.0 | — | | web-ts | web-ts | 100/100/100 | — | 100% / 100% / 1.0 | — | | oo-java | oo-java | 100/100/100 | — | 100% / 100% / 1.0 | — | | systems-go | systems-go | 100/100/100 | — | 100% / 100% / 1.0 | — | | deep-python (multi-hop) | scripting-python | 100/100/100 | 100% | 100% / 100% / 3.0 | — | | cross-lang-ts-rust | cross-lang | — | — | — | 100/100/100 | | cross-lang-grpc | cross-lang | — | — | — | 100/100/100 | | cross-lang-queue | cross-lang | 100/100/100 | — | — | 100/100/100 | | cross-lang-pyo3 | cross-lang | 100/100/100 | — | — | 100/100/100 | | cross-lang-ws | cross-lang | 100/100/100 | — | — | 100/100/100 | Across 11 fixtures / 6 language families / 42 labeled symbols (all resolved): pooled call edges **precision 100% / recall 94% / F1 97%** over 18 labeled edges; blast-radius **recall 100% with 0 distractors leaked**; affected-test **recall 100%** over the labeled linkages with the one labeled *unrelated* test correctly **not** selected; cross-language **precision 100% / recall 100% / F1 100%** over 6 labeled couplings with 6 distractor couplings (look-alike routes, a wrong-service gRPC stub, an unregistered PyO3 helper, ...) correctly **not** connected. Reading the numbers honestly: - **No false call edges were observed** in this 18-edge corpus (precision 100%); that is a result on the corpus, not a guarantee at scale. - **Recall is 100%** for Python/TypeScript/Java/Go, which resolve cross-file calls. The **50%** on Rust is real and expected: Rust call resolution is intra-file, so a module-qualified cross-file call is a true miss. Cross-file *reachability* is still preserved through `imports` edges, which is why blast-radius recall stays 100%. - **Blast radius is scored for noise, not just misses:** each seed labels distractor nodes that must stay out, and none leaked (100% exclusion); the average reported impact-set size equals the true affected-set size, so the walk is not over-broad. - **Affected-test selection is multi-hop:** the `deep-python` fixture changes a leaf three call hops below its test and still selects it, while a deliberately unrelated test is excluded (so recall is not bought with precision). - **Cross-language precision is earned across five boundary kinds:** a TypeScript `fetch("/session")` connects to the Rust axum handler that serves it (and a mounted `/api/users` client reaches its prefix-composed route); a Python gRPC client reaches its tonic server; a Kafka producer reaches its consumer; a Python `import` reaches its PyO3-exported Rust function; a JS WebSocket command reaches its C# handler — while every look-alike distractor (a `/sessions` path, a wrong-service stub, a wrong topic, an *unregistered* PyO3 helper, an unhandled message) is correctly left unconnected. The corpus is intentionally small and hand-verified; it validates extraction *correctness* on representative shapes, not internet-scale coverage. The [scale](#scale) section measures real repositories. See [BENCHMARKS.md](https://github.com/ColinVaughn/Synaptic/blob/HEAD/BENCHMARKS.md) for methodology and the ground-truth format. ### Prediction calibration The change-forecast layer attaches a confidence to each predicted co-change. `synaptic eval calibrate` measures whether that confidence is meaningful: it walks recent history, and for each commit uses every changed file as a seed, asks the predictor (trained only on prior commits) which files should co-change, then scores each prediction's confidence against what actually changed. It reports a **reliability table** (predicted vs. observed hit rate per confidence bin), a **Brier score**, the **Brier skill score** against an always-guess-the-base-rate baseline (so the Brier number is interpretable), and **expected calibration error**. This is a per-repo property: confidence reflects each repo's commit habits, so run it on yours. On this repo's own (squash-heavy, synthetic) history the skill score is **negative** — co-change prediction there is *worse than guessing the base rate*, because squashed commits touch many files at once and inflate apparent co-change. That is the metric working: it refuses to dress up a predictor that is miscalibrated on this history. Methodology in [BENCHMARKS.md](https://github.com/ColinVaughn/Synaptic/blob/HEAD/BENCHMARKS.md). ## Scale Extraction throughput across real OSS repositories spanning size tiers and language families, each cloned at a pinned SHA (`synaptic eval scale`; network + git, opt-in). Each timing is the median of 5 reps. The 2026-08-12 run covered **10 repositories, 9 language families, 783,928 supported LOC, 71,437 nodes, and 111,851 edges** with no skips. Warm throughput ranged from 44k to 339k LOC/s; median cold-to-warm speedup ranged from 1.4x to 2.8x. The largest checkout measured here, Humanizer (476,967 supported LOC), took 7.07s cold and 2.69s warm. Those are machine-specific development-worktree results, not universal or clean-release claims. "Cold" clears Synaptic's AST cache but the checkout and OS file cache were warm; incremental timing re-extracts a named unchanged source file and is not patch latency. Full method, per-repository results, limitations, exact SHAs, and raw samples are in [BENCHMARKS.md](https://github.com/ColinVaughn/Synaptic/blob/HEAD/BENCHMARKS.md). ## Extraction quality at scale Scale measures how *fast* extraction runs; a graph that anchored every declaration to the wrong line would post identical timings. `synaptic eval quality` measures whether the graph is **right**, across **60 pinned repositories covering all 39 shipped languages** (80,061 files, 938,001 nodes), using properties that need no hand labels: anchor exactness, parse and recovery health, determinism, incremental equivalence, and an independent universal-ctags comparison. The 2026-08-15 run: **pooled anchor exactness 735,198 / 735,493 (99.96%)**, with **60/60 repositories deterministic and incrementally equivalent** and no skips. 30 of 39 languages are exact on every checked declaration. The corpus is language-complete by construction — a test fails when a shipped extractor has no repository exercising it — and each repository carries pinned bounds, so a regression exits non-zero naming the repository and metric. The oracle is published as a symmetric difference, never a recall score: ctags is an independent second opinion, not ground truth. Method, per-language results, and the defects this benchmark found are in [BENCHMARKS.md](https://github.com/ColinVaughn/Synaptic/blob/HEAD/BENCHMARKS.md). ## Install Synaptic builds with a stable Rust toolchain (pinned to 1.97.1 via [rust-toolchain.toml](https://github.com/ColinVaughn/Synaptic/blob/HEAD/rust-toolchain.toml)). ```sh # From a clone, installs the `synaptic` binary onto your PATH: cargo install --path bin/synaptic # ...or build it in-tree: cargo build --release # -> target/release/synaptic ``` Prebuilt binaries for Linux/macOS/Windows are attached to each tagged [GitHub Release](https://github.com/ColinVaughn/Synaptic/blob/HEAD/../../releases) (see the `release` workflow). Optional integrations are behind feature flags (off by default): `pg` (Postgres introspection), `push` (live Neo4j/FalkorDB export), and `office` / `gws` / `media` (spreadsheet / Google-Workspace / audio-video ingest), e.g. `cargo install --path bin/synaptic --features pg,push`. See [Installation](https://github.com/ColinVaughn/Synaptic/wiki/Installation) and [Configuration](https://github.com/ColinVaughn/Synaptic/wiki/Configuration). Once installed, update in place with `synaptic self-update` (verifies a SHA-256 checksum and prompts before replacing the binary). Opt in to a background "update available" notice with `synaptic self-update --enable` — off by default, runs at most once a day, and never blocks normal commands. `cargo install` / source builds can self-update too, but the swap installs the default-feature prebuilt binary. ## Quickstart ```sh # 1. Build the graph for the current directory -> synaptic-out/ synaptic extract . # 2. Ask the graph a question (returns a relevant subgraph) synaptic query "authentication flow" # 3. What would changing a symbol break? (reverse impact) synaptic affected parse_config # 4. Serve the graph to an AI assistant over MCP synaptic serve ``` `extract` honors `.synapticignore` / `.gitignore` and skips sensitive files (`.env`, keys). A code-only corpus runs fully offline; the optional LLM semantic pass over docs and papers (`extract --semantic`) needs an API key (e.g. `OPENAI_API_KEY`). See [Quickstart](https://github.com/ColinVaughn/Synaptic/wiki/Quickstart). ## Output artifacts (`synaptic-out/`) | Artifact | What it is | |---|---| | `graph.json` | Full graph (node-link JSON), query it without re-reading files | | `GRAPH_REPORT.md` | God nodes, surprising connections, suggested questions, import cycles | | `graph.html` | Interactive 2D explorer (search + community color) | | `graph-3d.html` | Interactive 3D force graph (search, relation toggles, federation colors) | | `graph.svg` | Static layout (Barnes-Hut, component-packed, asset-shaped) | | `graph.graphml` / `graph.cypher` / `graph.dot` | Import into Gephi / Neo4j / Graphviz | | `callflow.html` / `tree.html` | Mermaid call-flow + D3 file tree | | `obsidian/`, `wiki/` | Obsidian vault / Markdown wiki (with `--obsidian` / `--wiki`) | ## Commands | Command | What it does | |---|---| | `extract [path]` | Build the graph and write `synaptic-out/`. Flags: `--directed`, `--obsidian`, `--wiki`, `--semantic` | | `export ` | Re-emit a format from an existing `graph.json` (no rebuild) or push live to Neo4j/FalkorDB | | `query ` | Return a relevance-ranked subgraph (each node scored). Flags: `--max-nodes`, `--repo`, `--dfs`, `--since ` (boost code changed on the branch), `--seed-changed`, `--json` | | `path ` | Shortest path between two nodes | | `explain ` | Show a node and its neighbours | | `affected ` | Nodes that (transitively) depend on a node; adds a caveat when a "0 dependents" symbol is reachable only via dynamic dispatch. Flags: `--depth`, `--relation` | | `hazards` | List reflection / dynamic-dispatch sites the graph records, so a "0 dependents" answer is not mistaken for "safe". Flags: `--repo`, `--kind`, `--limit` | | `search [synql]` | Structural search via SYNQL or a named `--pattern`. Flags: `--explain`, `--save`/`--saved`, `--json` | | `diff [rev2]` | Time-travel graph diff between two git revisions. Flags: `--since`, `--report`, `--html`, `--scope` | | `refactor ` | Plan a safe `rename`/`move`/`extract` for an agent, then `verify` the graph (never edits source) | | `predict [paths...]` | Forecast a change before applying it: blast radius, at-risk tests, risk, removed APIs, cycles. Flags: `--base`, `--edit ":"`, `--gate` | | `speculate [paths...]` | Run a change for real in a throwaway worktree: at-risk tests + a build/type-check, reporting pass/fail. Flags: `--patch`, `--test-cmd`, `--check-cmd` | | `audit readiness` | Static port/readiness audit: ranks framework sentinel returns, placeholders/stubs, generated-resource noise, and project metadata. Flags: `--profile`, `--severity`, `--repo`, `--json` | | `sql ` | `audit` SQL for performance + security over the SQL-aware graph, or `advise --query ""` on a candidate query before writing it. Flags: `--severity`, `--explain --db-url` (live EXPLAIN, needs `--features live-explain`) | | `eval replay [from]` | Replay history to score forecast quality against git ground truth (CI-gateable). Flag: `--min-test-recall` | | `eval quality` | Measure extraction correctness across the pinned real-world corpus, gated against per-repo baselines (network + git, opt-in). Flags: `--language`, `--repo`, `--pin`, `--update-baselines` | | `update [paths...]` | Incrementally rebuild after files change (`--full` for a full rebuild) | | `watch` | Rebuild automatically as files change (single repo; use `workspace build --watch` for a workspace) | | `serve` | Run the MCP server (stdio, or `--http --api-key `) | | `prs [number]` | Graph-aware PR dashboard / detail. Flags: `--triage`, `--conflicts`, `--base`, `--repo` | | `workspace ` | Multi-repo / monorepo federation (`init`/`add`/`discover`/`build`/`federate`/`coordinate`/`sync`/`status`/`list`). `build --watch` keeps a federated graph live across every member repo | | `global ` | The cross-repo global graph store (`~/.synaptic`) | | `memory ` | Ingest, record, search, compact, exchange, and evaluate durable source-grounded repository memory | | `api ` | Inventory API dependencies, discover contracts, measure coverage, scan changes, assess impact, and safely repair/verify/publish a draft PR | | `merge-graphs ` | Compose several `graph.json` files into one namespaced graph | | `ingest ` | Ingest an external source (cargo / mcp / scip / pg / url; `office` / `gws` / `media` behind feature flags) | | `hook ` | Manage git hooks + the `graph.json` merge driver | | `install` / `uninstall [platform]` | Install the Synaptic skill for a host assistant | | `cache ` | Maintain the on-disk extraction cache | | `self-update` | Update the binary from the latest GitHub release (opt-in). Flags: `--enable`/`--disable` (background notice), `--check`, `--yes` | The full reference with every flag is in [Commands](https://github.com/ColinVaughn/Synaptic/wiki/Commands). Run `synaptic --help` for the flag list at the terminal. ## Use it from an AI assistant (MCP) ```sh synaptic serve # stdio MCP server synaptic serve --http 127.0.0.1:8765 --api-key "$SYNAPTIC_API_KEY" # HTTP server synaptic serve --allow-memory-write # opt-in outcome recording synaptic serve --memory-principal reviewer \ --memory-repository-claim owner/repo # scope-filtered memory synaptic serve --graph promoted/graph.json --immutable-graph \ --expected-graph-sha256 "$GRAPH_SHA256" # authenticate exact loaded bytes synaptic serve --http 127.0.0.1:0 --ready-file /run/synaptic/ready.json # race-free child startup ``` The server exposes 30 core tools, five vulnerability tools, and five read-only repository-memory tools: graph navigation (`query_graph`, `get_node`, `get_source`, `get_neighbors`, `get_community`, `god_nodes`, `graph_stats`, `shortest_path`), impact analysis (`affected`, `find_callers`, `find_callees`, `find_references`, `dynamic_hazards`, `predict_impact`, `affected_tests`, `predict_edit`), federation (`list_repos`, `repo_stats`), change/PR review (`working_changes_impact`, `list_prs`, `get_pr_impact`, `triage_prs`), the advanced trio (`structural_search`, `time_travel_diff`, plan-only `plan_rename`), port/readiness audit (`readiness_audit`), and SQL auditing (`audit_sql`, `advise_sql`). Vulnerability work adds `vuln_check_dependency`, `vuln_findings`, `vuln_explain`, `vuln_scan`, and `vuln_brief`; a scan writes only with `record: true` and sends dependency coordinates to OSV only with `online: true`. On federated graphs, agents select a tag from `list_repos`; scans, findings, explanations, ledgers, and repair briefs are then isolated to that member, including external checkouts and Git-cached repositories. Artifact-only members are explicitly reported as not scannable. Memory retrieval adds `search_memory`, `explain_history`, `find_similar_change`, `known_pitfalls`, and `explain_decision`; `record_change_outcome` is advertised only with `--allow-memory-write`. It also serves MCP prompts, argument completions, resource templates and subscriptions, and a small REST surface (`/api/stats`, `/api/query`, ...) for non-MCP clients. Tool output is tuned to stay token-lean (terse defaults, capped lists); add `serve --concise` (or set `SYNAPTIC_CONCISE`) to lower the default sizes further. For digest-pinned or read-only deployments, `serve --immutable-graph --expected-graph-sha256 ` authenticates the exact byte buffer it parses and disables disk hot-reload, source catch-up, and filesystem watching. `--http 127.0.0.1:0 --ready-file ` binds before atomically publishing the kernel-assigned address, avoiding port reservation races in process supervisors. `synaptic install` wires the graph into a host assistant (a `PreToolUse` hook for Claude; a native MCP server for Codex, with `synaptic install codex --global` for the Codex desktop app). See [MCP Server](https://github.com/ColinVaughn/Synaptic/wiki/MCP-Server) and [Assistant Integration](https://github.com/ColinVaughn/Synaptic/wiki/Assistant-Integration). ## Languages 30+ languages via tree-sitter, each built and tested in isolation in CI: Python, JavaScript/TypeScript (+ JSX/TSX, Vue/Svelte/Astro), Go, Rust, Java, C#, Kotlin, Swift, C, C++, Objective-C, Ruby, PHP, Scala, Groovy, Lua, Dart, Elixir, Julia, Zig, Bash, PowerShell, Verilog, Fortran, CodeQL QL, and regex/delegation extractors for Classic ASP, Salesforce Apex, Pascal/Delphi, and Razor/Blazor. Plus data and project formats: SQL, JSON, YAML, HCL/Terraform, .NET project files (`.csproj`/`.sln`/`.slnx`), and Markdown structure. Framework-aware edges for PHP/Laravel and Dart/Flutter. Full breakdown in [Languages](https://github.com/ColinVaughn/Synaptic/wiki/Languages). ## Documentation The graph-native, vendor-neutral self-maintaining API workflow is documented in [API maintenance](https://github.com/ColinVaughn/Synaptic/blob/HEAD/docs/procedures/api-maintenance.md). The full documentation lives in the [project wiki](https://github.com/ColinVaughn/Synaptic/wiki): - **Getting started:** [Home](https://github.com/ColinVaughn/Synaptic/wiki/Home) - [Installation](https://github.com/ColinVaughn/Synaptic/wiki/Installation) - [Quickstart](https://github.com/ColinVaughn/Synaptic/wiki/Quickstart) - **Concepts:** [Architecture](https://github.com/ColinVaughn/Synaptic/wiki/Architecture) - [Languages](https://github.com/ColinVaughn/Synaptic/wiki/Languages) - **Using it:** [Commands](https://github.com/ColinVaughn/Synaptic/wiki/Commands) - [Extraction](https://github.com/ColinVaughn/Synaptic/wiki/Extraction) - [Querying](https://github.com/ColinVaughn/Synaptic/wiki/Querying) - [Analysis and Reports](https://github.com/ColinVaughn/Synaptic/wiki/Analysis-and-Reports) - [Output Formats](https://github.com/ColinVaughn/Synaptic/wiki/Output-Formats) - [Visualizations](https://github.com/ColinVaughn/Synaptic/wiki/Visualizations) - **Integrations:** [MCP Server](https://github.com/ColinVaughn/Synaptic/wiki/MCP-Server) - [Assistant Integration](https://github.com/ColinVaughn/Synaptic/wiki/Assistant-Integration) - [Ingestion](https://github.com/ColinVaughn/Synaptic/wiki/Ingestion) - [Semantic Analysis](https://github.com/ColinVaughn/Synaptic/wiki/Semantic-Analysis) - **Scaling:** [Workspaces and Federation](https://github.com/ColinVaughn/Synaptic/wiki/Workspaces-and-Federation) - [Incremental Updates](https://github.com/ColinVaughn/Synaptic/wiki/Incremental-Updates) - [PR Dashboard](https://github.com/ColinVaughn/Synaptic/wiki/PR-Dashboard) - **Reference:** [Configuration](https://github.com/ColinVaughn/Synaptic/wiki/Configuration) - [Development](https://github.com/ColinVaughn/Synaptic/wiki/Development) ## Development ```sh cargo test --workspace --all-features # all tests cargo fmt --all --check # formatting (enforced in CI) cargo clippy --workspace --all-targets --all-features -- -D warnings ``` The codebase is 27 library crates (`crates/*`) plus the `synaptic` binary (`bin/`). CI builds each language grammar in isolation so a grammar bump that silently drops nodes/edges fails on its own. See [Development](https://github.com/ColinVaughn/Synaptic/wiki/Development) and [Architecture](https://github.com/ColinVaughn/Synaptic/wiki/Architecture). ## Star History Star History Chart ## Community Questions, ideas, or want to show what you built? Join us on [Discord](https://discord.gg/ytX7R2PbNz). ## License GNU Affero General Public License, version 3 or later (`AGPL-3.0-or-later`), see [LICENSE](https://github.com/ColinVaughn/Synaptic/blob/HEAD/LICENSE) and [NOTICE](https://github.com/ColinVaughn/Synaptic/blob/HEAD/NOTICE). If you modify Synaptic and let users interact with it over a network, the license requires you to offer those users the corresponding source. Historical releases remain available under the licenses under which they were received. The separately maintained private Synaptic Platform site and B2B control plane are proprietary and are not covered by this repository's license.