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\n\n# SpecShip\n\n### Supercharge Claude Code with Semantic Code Intelligence\n\n**Stops your agent re-reading the codebase — structural answers in a few calls, not a grep-and-Read crawl · 100% local**\n\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![Self-contained](https://img.shields.io/badge/Node.js-bundled%20%C2%B7%20none%20required-brightgreen.svg)](https://nodejs.org/)\n\n[![Windows](https://img.shields.io/badge/Windows-supported-blue.svg)](#supported-platforms)\n[![macOS](https://img.shields.io/badge/macOS-supported-blue.svg)](#supported-platforms)\n[![Linux](https://img.shields.io/badge/Linux-supported-blue.svg)](#supported-platforms)\n\n[![Claude Code](https://img.shields.io/badge/Claude_Code-supported-blueviolet.svg)](#get-started)\n\n
\n\n## Get Started\n\n### 1. Install the CLI\n\nNo particular Node.js version to manage — the published install bundles its own runtime (Node 24 with FTS5, which SpecShip needs) and runs the same regardless of your system Node. You just need `npm` to fetch it:\n\n```bash\nnpm i -g @specship/specship@latest\n```\n\nOffline / air-gapped machine? No npm, no compiler, and no network needed. Every release is a **self-contained bundle** (a vendored Node runtime plus the app). On a connected machine, download the archive matching the offline machine's platform from the [Releases page](https://github.com/selvakumarEsra/specship/releases), copy it across, extract it, and run the installer baked inside:\n\n```bash\ntar -xzf specship-.tar.gz # or unzip specship-.zip on Windows\ncd specship-\n./install.sh # .\\install.ps1 on Windows\n```\n\nThat symlinks `specship` onto your `PATH`, then asks where to wire Claude Code — globally or a specific repo (`--global` / `--path ` for scripts) — using only the bundled runtime; nothing is compiled on the target. From a checkout, `./scripts/offline-install.sh ` (`.ps1` on Windows) does the same given a downloaded bundle. See [Offline / air-gapped install](https://specship.cc/getting-started/installation/#offline--air-gapped-install) for the full walkthrough.\n\n### 2. Wire up Claude Code\n\n```bash\nspecship install # full install: retrieval + spec-driven development\nspecship install --yes --location local # non-interactive, project-local\nspecship install --with-jira --with-designer # also enable the optional integrations\nspecship install --no-sdd # retrieval-only (skip the spec-driven layer)\n```\n\n`specship install` is **wiring-only** — it never installs the binary or touches npm (get the CLI via step 1, or the offline bundle). It writes the SpecShip MCP server into `~/.claude.json` (global) or `./.mcp.json` (project-local; `--path ` targets a specific repo), the auto-allow permissions list into Claude's `settings.json`, all slash commands, the spec-driven-development steering (on by default; `--no-sdd` opts out), a per-prompt nudge that steers the agent to the graph before Read/Grep, and a session-start cheat-sheet of SpecShip's commands (`SPECSHIP_NO_CHEATSHEET=1` to silence). The two integrations that talk to an external service — **JIRA** (your Atlassian instance) and **Designer** (claude.ai, experimental) — are strictly opt-in via `--with-jira` / `--with-designer`, and a later plain re-install preserves them.\n\n
\nEnvironment variables — every runtime switch\n\nSet the behavior switches durably in SpecShip's own settings files — `/.specship/settings.json` (per project, wins) or `~/.specship/settings.json` (machine-wide) — with env-var names as keys:\n\n```json\n{ \"SPECSHIP_NO_STEERING\": \"1\" }\n```\n\nAn actual environment variable (shell `export`, or Claude Code's `settings.json` `env` block) overrides both files for one-off use.\n\n| Variable | What it does |\n|---|---|\n| `SPECSHIP_NO_STEERING=1` | Turn off the per-prompt \"use the graph first\" nudge |\n| `SPECSHIP_NO_CHEATSHEET=1` | Turn off the session-start cheat-sheet of SpecShip commands |\n| `SPECSHIP_NO_STATUSLINE_TIPS=1` | Turn off the rotating usage tip on the status-line segment |\n| `SPECSHIP_COMPACT=0` | Disable the smaller-model output compaction entirely |\n| `SPECSHIP_MODEL=` | Force the model tier for compaction (normally auto-detected) |\n| `SPECSHIP_INTEGRATIONS` | Written by the installer for `--with-jira`/`--with-designer` — which optional tool groups the MCP server exposes |\n| `SPECSHIP_WATCH_DEBOUNCE_MS` | Auto-sync debounce window (default 2000, clamped 100ms–60s) |\n| `SPECSHIP_NO_DAEMON=1` | Disable the file watcher (sandboxed environments) |\n\nThe full generated list lives in the [CLI reference](https://specship.cc/reference/cli/#environment-variables).\n\n
\n\n### Gemini CLI\n\nSpecShip's MCP server is agent-neutral, so Gemini CLI can talk to it too. Install it the same way, naming the target:\n\n```bash\nspecship install --target gemini # Gemini CLI only\nspecship install --target claude,gemini # both agents\n```\n\nA plain `specship install` still wires Claude Code alone — Gemini is opt-in. The install writes the `specship` entry into your Gemini settings file (`~/.gemini/settings.json` globally, `/.gemini/settings.json` with `--location local`), preserving any other MCP servers and settings already there, and `specship uninstall --target gemini --keep-data` removes exactly that entry.\n\n
\nPrefer to paste it in by hand?\n\nPrint the snippet:\n\n```bash\nspecship install --print-config --target gemini # global (~/.gemini/settings.json)\nspecship install --print-config --target gemini --location local # this project (.gemini/settings.json)\n```\n\nThen paste the `mcpServers` block into your Gemini CLI settings file and restart Gemini CLI:\n\n```json\n{\n \"mcpServers\": {\n \"specship\": {\n \"command\": \"specship\",\n \"args\": [\"serve\", \"--mcp\"]\n }\n }\n}\n```\n\n- **Every project (global):** `~/.gemini/settings.json`\n- **One project only:** `/.gemini/settings.json`\n\nIf the file already exists, merge the `specship` entry into your existing `mcpServers` object rather than replacing the file.\n\n
\n\nYou still need `specship init -i` in each project (step 3) so there's an index to query.\n\nVerified against Gemini CLI 0.56.0. This gives Gemini CLI the SpecShip **MCP tools** only — the Claude Code install additionally wires slash commands, auto-sync hooks, the retrieval-steering nudge, the `specship-explorer` subagent, and the status-line segment, none of which have a Gemini equivalent here. Retrieval benchmarks were measured on Claude Code.\n\n### 3. Initialize each project\n\n```bash\ncd your-project\nspecship init -i\n```\n\n`specship init` creates the local `.specship/` index directory; adding `-i` (`--index`) also builds the initial graph in the same step. Without `-i`, run `specship index` afterwards.\n\n### Uninstall\n\n```bash\nspecship uninstall\n```\n\nCompletely removes SpecShip — the Claude Code wiring, this project's index, your `~/.specship` data (including saved JIRA credentials and worktrees), and the `specship` binary itself — after showing exactly what will be deleted and asking to confirm (`--yes` skips the prompt). Use `specship uninstall --keep-data` to only unwire from Claude Code and keep everything else. Indexes in other projects aren't auto-discovered — remove those per-project with `specship uninit`.\n\n---\n\n## Specs as First-Class Citizens\n\nWrite requirements in Markdown under `specs/` with embedded IDs, and SpecShip indexes them alongside the code. Each spec becomes a queryable node with a content-hashed body, parent/child structure, and links to the code that implements it.\n\n```markdown\n\n---\nid: AUTH-DOC\ntitle: Authentication\n---\n\n# Login must rate-limit failed attempts\n\nThe login endpoint rejects more than 5 failed attempts per IP per minute.\n```\n\nAfter `specship init -i`, the agent can:\n\n- `mcp__specship__specship_spec(\"REQ-AUTH-001\")` — fetch spec + linked code + state\n- `mcp__specship__specship_link_assert(...)` — declare a link after implementing\n- `mcp__specship__specship_drifted` — review queue when spec or code moves\n\nThe link layer carries state — `implemented`, `verified`, `drifted`, `broken`, `orphaned` — keyed on logical identity (file + qualified name) so links survive ordinary refactors. Drop `// @implements REQ-AUTH-001` in your code as a backstop when the agent forgets to assert.\n\n```bash\nspecship drifted # review queue\nspecship drifted --fail-on=broken,drifted # CI gate\n```\n\n### Spec-driven workflows\n\nA YAML workflow engine (`specship workflow run `) drives the agent through deterministic spec → implement → verify → link loops in an isolated git worktree, with approval gates so a non-coding spec author reviews the plan and final diff. Four bundled workflows ship by default:\n\n- `spec-implement` — plan → approve → implement → test → link → final review\n- `spec-fix` — diagnose a drifted link → fix code → re-verify\n- `spec-verify` — run tests, promote `implemented` links to `verified`\n- `spec-relink` — re-attach an orphan after a refactor\n\nCustomize by dropping your own `/.specship/workflows/.yaml` (project tier overrides bundled defaults). The matching slash commands `/specship:spec`, `/ss-implement`, `/ss-drifted`, `/ss-fix`, `/ss-relink` are installed into Claude Code by `specship install`.\n\n---\n\n## Self-Improving, With You in the Loop\n\nSpecShip observes your Claude Code sessions and gets smarter every time you use it — without ever changing anything behind your back:\n\n- **It crystallizes what worked.** A completed multi-step workflow run becomes a reusable recipe proposal; a command you kept correcting into a working form becomes a \"use this form\" rule; recurring corrections are captured with the context they followed. Run `/specship:learn` to crystallize the current session's workflow on demand.\n- **Everything is a human-gated proposal.** Each one shows a preview diff of exactly what it would write (a CLAUDE.md rule, a memory note, a slash command, a hook); nothing lands until you apply it, and every apply is undoable. Review from the dashboard's **Improvements** page or `specship reflect`.\n- **It remembers your work.** A four-tier SQLite memory — the code **graph** (deterministic truth), your **specs** (human-confirmed intent), the full **task history** (every session, tool call, cost, outcome), and the **crystallized rules/skills** you approved. `specship_explore` surfaces a \"Prior work\" section when past sessions edited the files at hand, so the agent starts from what was already done.\n- **Deterministic and local.** Proposals cite the actual sessions that triggered them; recall is a SQL join, never an LLM summary; nothing leaves your machine.\n\n---\n\n## Why SpecShip?\n\nWhen Claude Code explores a codebase, it spawns **Explore agents** that scan files with grep, glob, and Read — consuming tokens on every tool call.\n\n**SpecShip gives those agents a pre-indexed knowledge graph** — symbol relationships, call graphs, and code structure. Agents query the graph instantly instead of scanning files.\n\n## Key Features\n\n| | |\n|---|---|\n| **Smart Context Building** | One tool call returns entry points, related symbols, and code snippets — no expensive exploration agents |\n| **Full-Text Search** | Find code by name instantly across your entire codebase, powered by FTS5 |\n| **Impact Analysis** | Trace callers, callees, and the full impact radius of any symbol before making changes |\n| **Always Fresh** | File watcher uses native OS events (FSEvents/inotify/ReadDirectoryChangesW) with debounced auto-sync — the graph stays current as you code, zero config |\n| **20+ Languages** | TypeScript, JavaScript, Python, Go, Rust, Java, C#, PHP, Ruby, C, C++, Objective-C, Swift, Kotlin, Dart, Lua, Luau, Svelte, Liquid, Pascal/Delphi |\n| **Framework-aware Routes** | Recognizes web-framework routing files and links URL patterns to their handlers across 14 frameworks |\n| **Desktop UI** | Live dashboard for cost, drift, tool-call heatmap, cache analytics, SpecShip token impact, plus a project picker that auto-discovers every project you've used Claude Code in |\n| **Self-Improving** | Mines your sessions for what worked and what wasted — and proposes rules, skills, and hooks you approve with a preview diff. Prior-work recall built into every explore |\n| **100% Local** | The core never leaves your machine — no API keys, no external services, SQLite only. The two optional integrations that do talk to a service (JIRA → your Atlassian instance, Designer → claude.ai, experimental) are strictly opt-in: `specship install --with-jira` / `--with-designer` |\n\n
\nHow auto-syncing works — and why you don't need to run specship sync manually\n\nWhen Claude Code launches `specship serve --mcp`, three layers keep the index in step with your code — and make sure the agent never gets a silent wrong answer in the brief window between an edit and the next sync:\n\n1. **File watcher with debounced auto-sync.** A native FSEvents / inotify / ReadDirectoryChangesW watcher captures every source-file create / modify / delete and triggers a re-index after a debounce window (default `2000ms`, tunable via `SPECSHIP_WATCH_DEBOUNCE_MS`, clamped to `[100ms, 60s]`). Bursts of edits collapse into a single sync.\n\n2. **Per-file staleness banner.** During the brief debounce window, MCP tool responses that would reference a still-pending file prepend a `⚠️` banner naming it and telling the agent to `Read` it directly. Pending files NOT referenced by the response surface as a small footer instead. Either way, the agent gets an explicit signal — validated with Claude Code, where the agent literally says \"Reading the file directly for the live content\" before opening it.\n\n3. **Connect-time catch-up.** When the MCP server (re)connects, specship runs a fast `(size, mtime)` + content-hash reconciliation against the working tree before answering the first query — so edits made while no MCP server was running (a `git pull` from the terminal, edits from another editor, a previous agent session that exited) get absorbed on the next session's first tool call.\n\n```\nagent writes src/Widget.ts\n → watcher fires (<100ms)\n → debounce (default 2s)\n → sync; Widget.ts is in the index\n → next agent query sees it\n```\n\n**Verify any time** with `specship_status` (via MCP) or `specship status` (CLI). If anything is pending, you'll see a `### Pending sync:` section naming the files and their edit age.\n\nThe handful of cases where manual `specship sync` makes sense: the watcher is disabled (sandboxed environments, or `SPECSHIP_NO_DAEMON=1`), or you're scripting against the index outside an agent session and want a pre-flight sync at the start of your script.\n\n\n
\n\n---\n\n## Dashboard\n\n`specship desktop` boots a single-process Fastify server that renders the dashboard **server-side** on `http://127.0.0.1:4242/`. One port serves both the API and the dashboard. No Electron, no SPA build, no auth — loopback only, and its dependency tree stays lean enough to install behind a locked-down registry.\n\n![SpecShip Desktop dashboard — stat tiles, recent neighborhood mini-graph, tips, tool-call heatmap and recent-prompt rollup at a glance](https://raw.githubusercontent.com/selvakumarEsra/specship/main/assets/screenshots/dashboard.png?v=1)\n\nThe dashboard is designed to answer four questions in one glance — **what is the structural state of my codebase, what needs attention, what did my last session cost, and what should I do about it.** The zones, top-to-bottom:\n\n#### Status strip · top of every page\n\nProject path · backend (`better-sqlite3` / `node:sqlite`) · node count · edge count · drift count · last-index time. Always visible — drift > 0 turns amber, index time pulses red after 30 minutes of staleness.\n\n#### Project picker · top bar\n\nAuto-discovers every project under `~/.claude/projects/`, decodes the slug back to its absolute path, flags each one with `initialized` / `not init` / `missing`, and shows the most-recently-touched first. A live SSE stream pushes new entries the moment you open a project in Claude Code — no refresh. Pick one and every codegraph-scoped surface (status, graph, specs, drift, workflows, memory) switches to that project's data.\n\n#### Stat tiles · 4 across\n\n| Tile | Surfaces |\n|---|---|\n| **Last session cost** | Total $ for your most recent Claude Code session, sourced from the JSONL transcripts ingested in the background. Click → Sessions page with that session focused. |\n| **Tool calls · range** | Count of tool calls in the selected time range (Today / This week / This month / All time, picker top-right). Click → Heatmap. |\n| **Subagent spend** | What % of your token spend went to Task-tool subagents. Hot signal: above ~40 % usually means a workflow is over-delegating. Click → Heatmap → Subagents lane. |\n| **Drift queue** | Spec-link rows in `drifted`, `broken`, or `orphaned` state. Click → Drift queue. The sidebar item also carries this badge so it's visible from any page. |\n\n#### Recent neighborhood · interactive mini-graph\n\nA small live `` panel — pan/zoom, click any node to deep-link into `/graph?focus=`. By default it shows a 15–25 node slice around the file you most recently edited. When the API returns no rows (fresh dev, no project indexed), it falls back to a seed neighborhood with all four node kinds (purple `code` / blue `spec` / green `test` / teal `route`) and a drifted spec, so the visual language is always on screen.\n\n#### Tips panel\n\nRule-based pattern-matcher over your transcripts. Each tip has a severity bar (`error` / `warn` / `info`), a one-line title, a concrete `Fix` (often a copyable command), and an estimated saving. Examples that show up in real usage:\n\n> _You read `auth.ts` 17 times last session. Same answer via `specship_explore` in 1 call._\n>\n> _Bash(grep) returned 82k tokens. `specship_search` covers this in 600._\n>\n> _Cache miss rate on your evening sessions is 91%. Could be your system prompt drifts each turn._\n\n`Apply` jumps to the related surface; `Dismiss` snoozes the tip (snooze persistence lands in the next release).\n\n#### Tool-call heatmap strip\n\nOne cell per touched file, sized roughly by path length so longer paths get more room. Color intensity tracks tool-call volume in the selected range. Hover for the path + counts; click to drill into the file's tool breakdown with a sessions list and a \"heavy tool\" callout (e.g. _\"`Read` returned 396 k tokens here — a structural query would cover it in a fraction\"_).\n\n#### Recent prompts · by cost\n\nLast 8–12 user prompts across your sessions, with a per-prompt cost bar and token rollup. Expensive prompts pop red; cache-hit % shows next to each. Click a row to jump into the Sessions deep-dive scrolled to that prompt — token-split micro-bars, every tool call with its result-token weight, and tagged \"heavy tool\" rows.\n\n#### Cache analytics card\n\nOne big number — your **cache read rate** — plus a 2×2 breakdown: creation tokens (with 1h / 5m split), read tokens (charged at ~10 %), estimated dollars saved this week, week-over-week delta. The single biggest controllable knob for keeping Claude Code cheap, surfaced where you can see it without going hunting.\n\n> **Project & time scope.** Every numeric on this page respects the project picker's active selection and the range selector top-right. Switching projects re-fetches without a page reload.\n\n#### SpecShip Impact · is SpecShip earning its keep?\n\nA dedicated page that puts SpecShip's own token cost next to what it saved, per prompt → session → project → all-projects (the Session Detail page carries the same per-prompt chip and per-session line). Two numbers, deliberately kept apart:\n\n- **Spend — measured.** The exact tokens SpecShip's own tool calls put into the conversation.\n- **Saved — estimated.** For each code-graph query, the size of the files its symbols live in — what a `Read` of them would have cost — deduplicated per prompt.\n\n**\"Saved\" is a conservative lower bound.** It credits only a single direct read of the named files, *not* the multi-call grep + read exploration (re-reads, dead-ends, extra turns) SpecShip actually replaces — the end-to-end win that the [benchmarks](#why-specship) measure with a with-vs-without comparison. So treat spend as exact and saved as a floor; a fixed per-session tool-definition overhead is shown separately, and every estimate is marked `est.`.\n\n#### Beyond the dashboard\n\nSame shell, same shortcuts, more depth:\n\n| Surface | What |\n|---|---|\n| **Graph** | Full xyflow code explorer — pan/zoom, fuzzy search, kind filters, click-to-recenter, side panel with callers / callees / linked specs / \"Reveal in editor\". Hierarchical / Force / Spec-anchored layouts. |\n| **Specs** | Doc tree + Markdown spec detail; per-spec linked-code list with state pills and one-click `Implement` / `Verify` / `Edit spec` / `Show in graph` actions. |\n| **Drift queue** | Filterable list of links needing attention. Bulk re-verify, bulk re-attach via the relink workflow. |\n| **Workflows + Runs** | Run any bundled or project-tier workflow, watch its DAG advance live via SSE, approve / reject pause gates, inspect per-step artifacts (plan.md, diff.md, test_results.md). |\n| **Sessions / Heatmap / Costs / Compare / Tips** | The Claude Code analytics suite — sessions deep-dive with per-prompt expand, file/tool/subagent heatmap drilldowns, per-day cost line + by-model donut, cross-project comparison. |\n| **SpecShip Impact** | Measured tokens SpecShip's tools spent vs. an estimated (conservative) count of tokens saved, per prompt / session / project / all-projects, with a spend-vs-saved trend and per-tool breakdown. |\n| **Memory** | The full `CLAUDE.md` hierarchy (managed / user / project / subdir) plus `@import` resolution plus `~/.claude/memory/*.md` agent-written notes. Sources view + Effective (merged-precedence) view. |\n| **Design system** | The visual reference for the entire app — every token, palette swatch, semantic state, button/pill family, and the 4 px node-color legibility test that the graph relies on. |\n\nA live boot splash animates the Wake logomark assembling on first launch each session — then fades into the dashboard. Subsequent reloads within the same session skip straight to the dashboard.\n\n---\n\n## Framework-aware Routes\n\nSpecShip detects web-framework routing files and emits `route` nodes linked by `references` edges to their handler classes or functions. Querying callers of a view/controller now surfaces the URL pattern that binds it.\n\n| Framework | Shapes recognized |\n|---|---|\n| **Django** | `path()`, `re_path()`, `url()`, `include()` in `urls.py` (CBV `.as_view()`, dotted paths) |\n| **Flask** | `@app.route('/path', methods=[...])`, blueprint routes |\n| **FastAPI** | `@app.get(...)`, `@router.post(...)`, all standard methods |\n| **Express** | `app.get(...)`, `router.post(...)` with middleware chains |\n| **NestJS** | `@Controller` + `@Get/@Post/...`, GraphQL `@Resolver` + `@Query/@Mutation`, `@MessagePattern`/`@EventPattern`, `@SubscribeMessage` |\n| **Laravel** | `Route::get()`, `Route::resource()`, `Controller@action`, tuple syntax |\n| **Drupal** | `*.routing.yml` routes (`_controller`, `_form`, entity handlers); `hook_*` implementations in `.module`/`.theme`/`.install`/`.inc` |\n| **Rails** | `get '/x', to: 'users#index'`, hash-rocket `=>` syntax |\n| **Spring** | `@GetMapping`, `@PostMapping`, `@RequestMapping` on methods |\n| **Gin / chi / gorilla / mux** | `r.GET(...)`, `router.HandleFunc(...)` |\n| **Axum / actix / Rocket** | `.route(\"/x\", get(handler))` |\n| **ASP.NET** | `[HttpGet(\"/x\")]` attributes on action methods |\n| **Vapor** | `app.get(\"x\", use: handler)` |\n| **React Router** / **SvelteKit** | Route component nodes |\n\n---\n\n## Quick Start\n\n```bash\nnpm i -g @specship/specship@latest\nspecship install --yes # writes ~/.claude.json + ~/.claude/settings.json\ncd your-project && specship init -i\n# restart Claude Code\n```\n\nThe installer:\n- Writes Claude Code's MCP server config (`~/.claude.json` for global, `./.mcp.json` for project-local)\n- Writes the auto-allow permissions list into `~/.claude/settings.json`\n- For local installs, also runs `specship init` against the current directory\n\n**Non-interactive (scripting / CI):**\n\n```bash\nspecship install --yes # global, auto-allow on\nspecship install --location=local --yes # project-local\nspecship install --print-config # print snippet, no file writes\nspecship install --print-config --target gemini # Gemini CLI settings snippet\nspecship install --no-permissions # skip auto-allow list\n```\n\n| Flag | Values | Default |\n|---|---|---|\n| `--location` | `global`, `local` | prompt |\n| `--yes` | (boolean) | prompt every step |\n| `--no-permissions` | (boolean) skip Claude auto-allow list | permissions on |\n| `--print-config` | dump the MCP snippet and exit (no file writes) | — |\n| `--target` | `claude`, `gemini` — which snippet `--print-config` prints | `claude` |\n\n
\nManual Setup (Alternative)\n\n**Install globally:**\n```bash\nnpm install -g @specship/specship@latest\n```\n\n**Add to `~/.claude.json`:**\n```json\n{\n \"mcpServers\": {\n \"specship\": {\n \"type\": \"stdio\",\n \"command\": \"specship\",\n \"args\": [\"serve\", \"--mcp\"]\n }\n }\n}\n```\n\n**Add to `~/.claude/settings.json` (optional, for auto-allow):**\n```json\n{\n \"permissions\": {\n \"allow\": [\n \"mcp__specship__specship_search\",\n \"mcp__specship__specship_explore\",\n \"mcp__specship__specship_callers\",\n \"mcp__specship__specship_callees\",\n \"mcp__specship__specship_impact\",\n \"mcp__specship__specship_node\",\n \"mcp__specship__specship_status\",\n \"mcp__specship__specship_files\"\n ]\n }\n}\n```\n\n
\n\n
\nAgent Tool Guidance\n\nSpecShip's MCP server delivers its usage guidance to Claude Code **automatically**, in the MCP `initialize` response — there's no instructions file to manage and nothing is added to your `CLAUDE.md`. In short, it tells the agent to:\n\n- **Answer structural questions directly with SpecShip** — it *is* the pre-built index, so a grep/read loop just repeats work it already did. Treat the returned source as already read.\n- **Pick the tool by intent:** `specship_explore` for almost anything — \"how does X work\", a flow/\"how does X reach Y\", or surveying an area (one call returns the relevant symbols' source grouped by file); `specship_search` to just locate a symbol; `specship_callers`/`specship_callees` to walk call flow; `specship_impact` before editing; `specship_node` for one specific symbol's full source (it returns every overload for an ambiguous name).\n- **Trust the results — don't re-verify with grep**, and check the staleness banner after edits.\n- If `.specship/` doesn't exist yet, offer to run `specship init -i`.\n\nThe exact text is `src/mcp/server-instructions.ts` — the single source of truth.\n\n
\n\n---\n\n## How It Works\n\n```\n┌───────────────────────────────────────────────────────────────────┐\n│ Claude Code │\n│ │\n│ \"How does a request reach the database?\" │\n│ calls SpecShip tools directly — no Explore sub-agent │\n│ │ │\n└─────────────────────────────────┬─────────────────────────────────┘\n │\n ▼\n┌───────────────────────────────────────────────────────────────────┐\n│ SpecShip MCP Server │\n│ │\n│ explore · search · callers · callees · impact · node │\n│ │ │\n│ ▼ │\n│ SQLite knowledge graph │\n│ symbols · edges · files · FTS5 full-text search │\n└───────────────────────────────────────────────────────────────────┘\n```\n\n1. **Extraction** — [tree-sitter](https://tree-sitter.github.io/) parses source code into ASTs. Language-specific queries extract nodes (functions, classes, methods) and edges (calls, imports, extends, implements).\n\n2. **Storage** — Everything goes into a local SQLite database (`.specship/specship.db`) with FTS5 full-text search.\n\n3. **Resolution** — After extraction, references are resolved: function calls → definitions, imports → source files, class inheritance, and framework-specific patterns.\n\n4. **Auto-Sync** — The MCP server watches your project using native OS file events. Changes are debounced (2-second quiet window), filtered to source files only, and incrementally synced. The graph stays fresh as you code — no configuration needed.\n\n---\n\n## CLI Reference\n\n```bash\nspecship # Run interactive installer\nspecship install # Run installer (explicit)\nspecship uninstall # Completely remove SpecShip (wiring + index + ~/.specship + binary; --keep-data to only unwire)\nspecship init [path] # Initialize in a project (--index to also index)\nspecship uninit [path] # Remove SpecShip from a project (--force to skip prompt)\nspecship index [path] # Full index (--force to re-index, --quiet for less output)\nspecship sync [path] # Incremental update\nspecship status [path] # Show statistics\nspecship query # Search symbols (--kind, --limit, --json)\nspecship files [path] # Show file structure (--format, --filter, --max-depth, --json)\nspecship callers # Find what calls a function/method (--limit, --json)\nspecship callees # Find what a function/method calls (--limit, --json)\nspecship impact # Analyze what code is affected by changing a symbol (--depth, --json)\nspecship affected [files...] # Find test files affected by changes (see below)\nspecship jira configure # Connect to JIRA (--base-url, --email/--api-token or --pat, --deployment, --project)\nspecship jira test # Verify the connection + validate configured transition names against your workflow\nspecship jira track # Status of issues SpecShip has picked (--project, --path)\nspecship jira transition [state] # Move an issue to a state, or list its available transitions (--list)\nspecship jira release # Stamp a fixVersion + \"shipped in\" comment onto issues (--keys, --project)\nspecship memory capture # Capture a lesson/anti-pattern as a reviewable memory rule (--title, --target; text on stdin)\nspecship memory list # List the memory rules SpecShip has applied\nspecship memory remove # Remove a memory rule (previewed; --yes to write)\nspecship memory edit # Replace a memory rule's body (previewed; --yes to write)\nspecship serve --mcp # Start MCP server\n```\n\n### `specship affected`\n\nTraces import dependencies transitively to find which test files are affected by changed source files.\n\n```bash\nspecship affected src/utils.ts src/api.ts # Pass files as arguments\ngit diff --name-only | specship affected --stdin # Pipe from git diff\nspecship affected src/auth.ts --filter \"e2e/*\" # Custom test file pattern\n```\n\n| Option | Description | Default |\n|--------|-------------|---------|\n| `--stdin` | Read file list from stdin | `false` |\n| `-d, --depth ` | Max dependency traversal depth | `5` |\n| `-f, --filter ` | Custom glob to identify test files | auto-detect |\n| `-j, --json` | Output as JSON | `false` |\n| `-q, --quiet` | Output file paths only | `false` |\n\n**CI/hook example:**\n\n```bash\n#!/usr/bin/env bash\nAFFECTED=$(git diff --name-only HEAD | specship affected --stdin --quiet)\nif [ -n \"$AFFECTED\" ]; then\n npx vitest run $AFFECTED\nfi\n```\n\n---\n\n## MCP Tools\n\nWhen running as an MCP server, SpecShip exposes these tools to Claude Code:\n\n| Tool | Purpose |\n|------|---------|\n| `specship_explore` | **Primary.** Answer almost any question in one call — \"how does X work\", a flow (\"how does X reach Y\"), or surveying an area — returning the relevant symbols' verbatim source grouped by file, plus a relationship map and blast radius. Surfaces dynamic-dispatch hops (callbacks, React re-render, interface→impl) grep can't follow. |\n| `specship_search` | Find symbols by name across the codebase |\n| `specship_callers` | Find what calls a function |\n| `specship_callees` | Find what a function calls |\n| `specship_impact` | Analyze what code is affected by changing a symbol |\n| `specship_node` | Get one specific symbol's details + full source (returns every overload for an ambiguous name) |\n| `specship_files` | Get indexed file structure (faster than filesystem scanning) |\n| `specship_status` | Check index health and statistics, plus server identity — version, install method, where it was loaded from, node version |\n| `specship_health` | Code-health report — maintainability (coupling hotspots, god files, cycles, dead code) and fitness (dependency/layering rules), filterable via `checks` |\n\nThe JIRA integration adds fourteen more (`specship_jira_issues`, `_issue`, `_pick`, `_start`, `_track`, `_publish`, `_transition`, `_add_task`, `_anchor`, `_epics`, `_coverage`, `_reconcile`, `_regression_pack`, `_regression_record`) — see below.\n\n---\n\n## JIRA Integration\n\nDrive work straight from your JIRA board without leaving the agent: list the\nissues assigned to you, pick one by its key, and let SpecShip turn it into a\nspec, run the implement-and-verify workflow, raise the pull request, and push\nthe status back to the ticket — so the board stays the source of truth. It works\nwith both **JIRA Cloud** (email + Atlassian API token) and **Data Center /\nServer** (Personal Access Token).\n\n**Connect once.** Credentials are stored at `~/.specship/jira.json` (owner-only,\n`0600`) — never in your project tree, never committed:\n\n```bash\n# Cloud\nspecship jira configure --base-url https://your-org.atlassian.net --email you@example.com --api-token \n# Data Center / Server\nspecship jira configure --base-url https://jira.your-company.com --pat \n\nspecship jira test # \"connected as \" — the token itself is never printed\n```\n\nFor headless / CI setups, every field can come from an environment variable\ninstead (`SPECSHIP_JIRA_BASE_URL`, `SPECSHIP_JIRA_EMAIL`,\n`SPECSHIP_JIRA_API_TOKEN`, `SPECSHIP_JIRA_PAT`, `SPECSHIP_JIRA_DEPLOYMENT`).\n\n**Then drive it from the agent.** You ask Claude Code in conversation and it\ncalls the JIRA MCP tools:\n\n| Tool | What it does |\n|------|--------------|\n| `specship_jira_issues` | List the issues assigned to you (resolved from your token — you never type your name); key, summary, status, type. Optional project filter. |\n| `specship_jira_issue` | Fetch one issue by key. |\n| `specship_jira_pick` | Draft a well-formed spec from an issue under `specs/` (summary → title, description → body, subtasks → acceptance criteria). Re-picking updates it in place. |\n| `specship_jira_start` | Run the spec-implement workflow on the generated spec; pauses at its plan/approve gate. |\n| `specship_jira_track` | A read-only table joining each picked issue's SpecShip work-state with its live JIRA status; flags specs edited in JIRA after publishing. |\n| `specship_jira_publish` | The reverse of pick — publish an authored spec back as a Story whose Sub-tasks mirror its acceptance criteria, key written into the spec. Idempotent. |\n| `specship_jira_transition` | Move an issue to a state its workflow offers, or list the options; an unavailable target is reported, never applied. |\n\nWhen the plan is approved **and** the implementation's tests pass, SpecShip\nraises a pull request with the GitHub CLI — the issue key rides the branch,\ntitle, and body so JIRA's development panel links it back. A failing run raises\nno PR, and the PR is never auto-merged or auto-closed (you decide Done). On start\nit assigns the issue to you and moves it toward \"In Progress\"; on PR raised it\nmoves it toward \"In Review\" and comments the PR link; as you verify acceptance\ncriteria, each proven one advances its published Sub-task toward Done. Transition\nnames are configurable — `specship jira test` validates them against your live\nworkflow, and `specship jira transition` drives any state by hand — and status\nwrite-back degrades gracefully when a transition doesn't exist. `specship jira\nrelease ` stamps a fixVersion + \"shipped in\" comment onto the issues.\nThe token is never logged and every request is locked to the host you configured.\n\nSee the [JIRA integration guide](https://specship.cc/guides/jira/) for the full\nwalkthrough.\n\n---\n\n## Library Usage\n\nSpecShip can be embedded directly. The npm package re-exports its programmatic\nAPI, so both `import` and `require` resolve the `SpecShip` class in your own\nprocess — handy for embedding it in an app (e.g. an Electron main process).\n\n```typescript\nimport SpecShip from '@specship/specship';\n// CommonJS works too:\n// const { SpecShip } = require('@specship/specship');\n\nconst cg = await SpecShip.init('/path/to/project');\n// Or: const cg = await SpecShip.open('/path/to/project');\n\nawait cg.indexAll({\n onProgress: (p) => console.log(`${p.phase}: ${p.current}/${p.total}`)\n});\n\nconst results = cg.searchNodes('UserService');\nconst callers = cg.getCallers(results[0].node.id);\nconst context = await cg.buildContext('fix login bug', { maxNodes: 20, includeCode: true, format: 'markdown' });\nconst impact = cg.getImpactRadius(results[0].node.id, 2);\n\ncg.watch(); // auto-sync on file changes\ncg.unwatch(); // stop watching\ncg.close();\n```\n\nLower-level building blocks are exported from the same entry point for callers\nthat drive the graph directly: `DatabaseConnection`, `QueryBuilder`,\n`getDatabasePath`, `initGrammars` / `loadGrammarsForLanguages`, and `FileLock`.\n\n**Embedding requirements**\n\n- Install from npm (`npm i @specship/specship@latest`) so the matching\n per-platform package — which carries the compiled library and its\n dependencies — is fetched alongside the shim.\n- The API runs on **your** runtime, so it needs **Node 22.5+** for the built-in\n `node:sqlite` (Electron qualifies when its bundled Node is 22.5+). The CLI and\n MCP server are unaffected — they run on the self-contained bundled runtime.\n- TypeScript types ship with the package. As with any Node-targeting library,\n keep `@types/node` available and `skipLibCheck: true` (the common default).\n\n---\n\n## Configuration\n\nThere isn't any — SpecShip is zero-config, with **no config file** to write or\nkeep in sync. Language support is automatic from the file extension; there's\nnothing to wire up per language.\n\nWhat it skips out of the box:\n\n- **Dependency, build, and cache directories** — `node_modules`, `vendor`,\n `dist`, `build`, `target`, `.venv`, `Pods`, `.next`, and the like across every\n [supported stack](#supported-languages) — so the graph is your code, not\n third-party noise. This holds even with no `.gitignore`.\n- **Anything in your `.gitignore`** — honored in git repos via git, and in\n non-git projects by reading `.gitignore` directly (root and nested).\n- **Files larger than 1 MB** — generated bundles, minified JS, vendored blobs.\n\nTo keep something else out, add it to `.gitignore`. To pull a default-excluded\ndirectory back **in** (say you really do want a vendored dependency indexed),\nadd a negation — `!vendor/`. The defaults apply uniformly, so committing a\ndependency or build directory doesn't force it into the graph; the `.gitignore`\nnegation is the explicit opt-in.\n\n## Supported Platforms\n\nEvery release ships a self-contained build (bundled Node runtime — nothing to\ncompile) for all three desktop OSes, on both Intel/AMD (x64) and ARM (arm64):\n\n| Platform | Architectures | Install |\n|----------|---------------|---------|\n| Windows | x64, arm64 | PowerShell installer or npm |\n| macOS | x64, arm64 | shell installer or npm |\n| Linux | x64, arm64 | shell installer or npm |\n\nSee [Get Started](#get-started) for the one-line install commands.\n\n## Supported Languages\n\n| Language | Extension | Status |\n|----------|-----------|--------|\n| TypeScript | `.ts`, `.tsx` | Full support |\n| JavaScript | `.js`, `.jsx`, `.mjs` | Full support |\n| Python | `.py` | Full support |\n| Go | `.go` | Full support |\n| Rust | `.rs` | Full support |\n| Java | `.java` | Full support |\n| C# | `.cs` | Full support |\n| PHP | `.php` | Full support |\n| Ruby | `.rb` | Full support |\n| C | `.c`, `.h` | Full support |\n| C++ | `.cpp`, `.hpp`, `.cc` | Full support |\n| Objective-C | `.m`, `.mm`, `.h` | Partial support (classes, protocols, methods, `@property`, `#import`, message sends; `.mm` ObjC++ may parse incompletely) |\n| Swift | `.swift` | Full support |\n| Kotlin | `.kt`, `.kts` | Full support |\n| Scala | `.scala`, `.sc` | Full support (classes, traits, methods, type aliases, Scala 3 enums) |\n| Dart | `.dart` | Full support |\n| Svelte | `.svelte` | Full support (script extraction, Svelte 5 runes, SvelteKit routes) |\n| Vue | `.vue` | Full support (script + script-setup extraction, Nuxt page/API/middleware routes) |\n| Liquid | `.liquid` | Full support |\n| Pascal / Delphi | `.pas`, `.dpr`, `.dpk`, `.lpr` | Full support (classes, records, interfaces, enums, DFM/FMX form files) |\n| Lua | `.lua` | Full support (functions, methods with receivers, local variables, `require` imports, call edges) |\n| Luau | `.luau` | Full support (everything in Lua, plus `type`/`export type` aliases, typed signatures, and Roblox instance-path `require`) |\n\n## Troubleshooting\n\n**\"SpecShip not initialized\"** — Run `specship init` in your project directory first.\n\n**Indexing is slow** — Check that `node_modules` and other large directories are excluded. Use `--quiet` to reduce output overhead.\n\n**MCP hits `database is locked`** — current builds shouldn't: SpecShip bundles its own Node runtime and uses Node's built-in `node:sqlite` in WAL mode, where concurrent reads never block on a writer. If you still see it:\n\n- **You're on an old (pre-0.9) install.** Reinstall: `npm i -g @specship/specship@latest`.\n\n**`specship status` shows `Journal:` other than `wal`** — WAL couldn't be enabled on this filesystem (common on network shares and WSL2 `/mnt`), so reads can block on writes. Move the project (with its `.specship/` folder) onto a local disk.\n**MCP server not connecting** — Ensure the project is initialized/indexed, verify the path in your MCP config, and check that `specship serve --mcp` works from the command line.\n\n**Missing symbols** — The MCP server auto-syncs on save (wait a couple seconds). Run `specship sync` manually if needed. Check that the file's language is supported and isn't inside a `.gitignore`d or default-excluded directory (e.g. `node_modules`, `dist`).\n\n## License\n\nMIT\n\n---\n\n
\n\n**Made for Claude Code**\n\n[Report Bug](https://github.com/selvakumarEsra/specship/issues) · [Request Feature](https://github.com/selvakumarEsra/specship/issues)\n\n
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