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Runs fully local.","maintainers":[{"name":"bg-myelixlabs","email":"brad@myelixlabs.com"},{"name":"bg-numarqe","email":"brad.garland@numarqe.com"},{"name":"da-numarqe","email":"david.alphen@numarqe.com"}],"readme":"# Synapse-MCP\n\n> A persistent code knowledge graph for AI agents. Query your codebase as a live graph — not as text files — so every AI session starts with context already built.\n\n---\n\n## Why This Exists\n\nAI coding agents have a hidden structural problem: **every conversation starts from scratch**.\n\nAsk an agent to trace a bug, review a change, or understand a subsystem, and it does something like this:\n\n1. Runs grep searches to find candidate files\n2. Reads those files in full, burning large portions of the context window\n3. Mentally reconstructs the call chain from raw text\n4. Guesses at what it might have missed and moves on\n\nOn a small codebase this is tolerable. On anything real it breaks down fast. The agent runs out of context window before it has the full picture. It can't know what calls what without reading both ends. It can't tell you what a function does without reading its body first. And when the conversation ends, everything it learned is thrown away.\n\nThis is the fundamental mismatch: **LLMs are stateless, codebases are not**.\n\n---\n\n## What Synapse Does\n\nSynapse-MCP is a persistent code knowledge graph that runs alongside your IDE. Rather than searching source text on demand, it continuously indexes your codebase into a structured graph of chunks, edges, embeddings, and summaries. When an AI agent needs to understand your code, it queries a pre-built model of it — the codebase is already understood before the question is asked.\n\nThe difference is not just speed. It is qualitative. A grep tool tells you where a word appears. Synapse answers *what does this subsystem do, what calls it, what tests cover it, and is it safe to change* — in under a second, without reading a single file.\n\n### Concrete before/after\n\n**Without Synapse** — agent asks \"what calls `invalidate_player_cache`?\":\n- 3–5 grep turns across the repo\n- 2–4 full file reads to confirm context\n- Reconstructed call chain from text, probably incomplete\n- 8–12 tool calls, ~2,000–6,000 tokens of context consumed\n\n**With Synapse** — same question:\n```\nsynapse_callers(symbol: \"invalidate_player_cache\")\n→ 3 direct callers with file:line, depth, and resolved symbols\n→ 1 tool call, ~200 tokens\n```\n\nThat ratio compounds across an entire session. Synapse does not make the agent slightly faster — it frees the context window for reasoning instead of reconstruction.\n\n---\n\n## The Compounding Advantage\n\nThe deeper differentiator is **persistence and accumulation**. Every summary written, every query that hits the cache, every call edge resolved — that is permanent signal that survives across restarts and across sessions.\n\n- Call `synapse_summarise` on a function once. Every future query against that chunk gets your explanation for free, forever.\n- Repeat queries return in under 10ms from a learning cache. The more a codebase is used with Synapse, the faster and more accurate it becomes.\n- After a few sessions of active use, Synapse has a working model of your codebase that reflects how it is actually used — not just what the source text says.\n\nA fresh agent session on a Synapse-indexed codebase is not starting from zero. It is inheriting everything every previous session contributed.\n\n---\n\n## Documentation\n\nThe [`docs/` overview](docs/README.md) is the canonical documentation entry\npoint. The directory contains several kinds of material; the notes below tell\ndevelopers and LLMs whether a file describes current architecture, operational\nprocedure, measured evidence, product positioning, or historical strategy.\n\n| Document | Purpose and intended use |\n| --- | --- |\n| [`docs/README.md`](docs/README.md) | **Start here.** Explains the product components, version domains, Free/Pro model, update model, and which detailed reference to read next. |\n| [`docs/indexer-optimisation.md`](docs/indexer-optimisation.md) | **Developer and LLM guardrails.** Records why the indexer, SQLite writer, edge resolver, telemetry, and Trunk lifecycle work as they do; includes invariants, rejected alternatives, limitations, and safe-change guidance. |\n| [`docs/architecture.md`](docs/architecture.md) | **Canonical architecture reference.** Maps the Node CLI, Rust launcher, Elixir runtime, hosted services, processes, installed state, and responsibility boundaries. |\n| [`docs/auto-update.md`](docs/auto-update.md) | **Canonical update reference.** Separates launcher and runtime updates and documents scheduling, activation, health checks, rollback, safety gates, and known gaps. |\n| [`docs/licensing.md`](docs/licensing.md) | **Canonical licensing reference.** Distinguishes software licensing from product entitlement and explains signed claims, devices, seats, Free/Pro artefacts, renewal, and offline behaviour. |\n| [`docs/local-dev-setup.md`](docs/local-dev-setup.md) | **Operational development runbook.** Covers local engine/auth setup, dev versus packaged launch modes, CLI commands, local builds, process cleanup, environment variables, and troubleshooting. |\n| [`docs/how-to-deploy-synapse-mcp.md`](docs/how-to-deploy-synapse-mcp.md) | **Commercial packaging and deployment design.** Contains resolved and proposed distribution, security, licensing, tiering, and hosted-service decisions; verify aspirational sections against current source before implementation. |\n| [`docs/aeon_synapse_comparison_to_no_synapse.md`](docs/aeon_synapse_comparison_to_no_synapse.md) | **Evidence and methodology.** Compares manual source exploration with Synapse-assisted analysis and records the measured calls, time, token use, completeness, and methodological limits. |\n| [`docs/marketing_pitch.md`](docs/marketing_pitch.md) | **Product positioning.** Presents benefits, benchmark claims, tool capabilities, compatibility, and pricing for marketing use; it is not an implementation contract. |\n| [`docs/monetization_and_distribution_plan.md`](docs/monetization_and_distribution_plan.md) | **Historical commercial strategy.** Explores packaging, pricing, feature gating, and distribution options; treat it as planning context where it differs from canonical architecture or current code. |\n\nWhen documents disagree with executable behaviour, use current production code\nand tests first, then the canonical technical references. Marketing and strategy\ndocuments describe intent and must not be assumed to represent shipped\nfunctionality.\n\n---\n\n## How Agents Use Synapse — Real Workflows\n\nSynapse is not a single search tool. It is an integrated workflow layer that replaces the grep → read → grep → read loop that dominates agent sessions today. Below are three real workflows showing the exact tool calls an agent makes with Synapse versus without it.\n\n### Workflow 1: Feature development — \"add a rate limit to the invite endpoint\"\n\n**Without Synapse** (typical agent session):\n1. `grep -r \"invite\"` → 47 results across controllers, tests, templates\n2. Read `play_controller.ex` (400 lines) to find the invite function\n3. `grep -r \"create_share_link\"` → find callers\n4. Read `api/play.ex` (600 lines) to understand the data layer\n5. `grep -r \"invite\" test/` → find existing test coverage\n6. Read 2–3 test files to understand the existing contract\n7. Guess at what other modules might be affected\n\n**Result:** 7+ tool calls, 3–4 full file reads, ~4,000 tokens of raw file content, incomplete picture.\n\n**With Synapse** (same task):\n```\n1. synapse_fast_context(query: \"invite endpoint rate limiting\")\n   → top 7 chunks with callers/callees attached, ~400ms\n\n2. synapse_edit_context(symbol: \"create_share_link/2\", intent: \"add rate limit\")\n   → must-read files, callers, callees, likely tests, behaviour boundaries, risk assessment\n\n3. synapse_tests_for(symbol: \"create_share_link/2\")\n   → galaxy_invite_steps.exs, 41_galaxy_share_link_invites.feature, ranked by confidence\n```\n\n**Result:** 3 tool calls, 0 file reads, ~600 tokens, complete picture including test contracts and safety boundaries.\n\n### Workflow 2: Bug investigation — \"singleflight cache is returning stale data\"\n\n**Without Synapse:**\n1. `grep -r \"singleflight\"` → find the module\n2. Read the full singleflight module (200+ lines)\n3. `grep -r \"get_or_compute\"` → find callers\n4. Read each caller file to trace the data flow\n5. `grep -r \"ets.insert\"` → find where the cache writes happen\n6. Read those files, try to reconstruct the write/read/invalidation lifecycle\n7. Still missing: what events does this emit? What tests cover this exact path?\n\n**With Synapse:**\n```\n1. synapse_behaviour_trace(query: \"get_or_compute_singleflight\", max_paths: 3)\n   → 3 ranked execution paths from entrypoint to target\n   → per-hop behaviour signals: ets_write, ets_lookup, telemetry_execute\n   → uncertainty gaps flagged where edges are inferred\n   → linked tests ranked by relevance\n\n2. synapse_impact(chunk_ids: [\"<singleflight_chunk_id>\"])\n   → blast radius: 12 transitive callers\n   → blind spots: 3 callers with no test coverage\n   → contract signals: ets_write + telemetry_execute flagged\n```\n\n**Result:** 2 tool calls, complete lifecycle trace with state read/write signals, no file reads needed.\n\n### Workflow 3: PR review — \"review this diff for safety\"\n\n**Without Synapse:**\n1. Read the diff (provided)\n2. For each changed file, `grep` to find what calls the changed functions\n3. Read those caller files to assess blast radius\n4. Manually search for related test files\n5. Read test files to check if the change is covered\n6. Try to assess whether state writes or events are affected (by reading source)\n7. Write review comments based on incomplete analysis\n\n**With Synapse:**\n```\n1. synapse_review(diff: \"<unified diff>\", repo_id: \"my_app\")\n   → ranked risks with risk_score and risk_level per affected node\n   → blind spots: uncovered callers sorted by risk\n   → total_tests_to_run: deduplicated, confidence-ranked test list\n   → contract_warnings: flags if changed code writes state or emits events\n   → recommended_action per risk (\"add test coverage before merging\")\n```\n\n**Result:** 1 tool call. The agent gets a complete review pack — blast radius, test gaps, contract warnings, and specific recommendations — without reading a single file beyond the diff itself.\n\n### The cost difference\n\n| Metric | Without Synapse | With Synapse |\n|---|---|---|\n| Tool calls per task | 8–15 | 1–3 |\n| File reads per task | 3–6 full files | 0 (graph-served) |\n| Context tokens consumed | 3,000–8,000 | 200–800 |\n| Information completeness | Partial, best-effort | Structural, with gap reporting |\n| Test coverage awareness | Manual grep, often missed | Automatic, confidence-ranked |\n| Persists across sessions | ❌ | ✅ |\n\n### Measured example: understanding the Synapse-MCP codebase itself\n\nWe tested this live — asking an agent to understand the full Synapse-MCP tool surface (29 tool modules, their capabilities, and how they connect).\n\n**Manual approach** — standard file browsing:\n\n| Step | Operation |\n|---|---|\n| 1 | `list_dir` tools directory → 29 file names |\n| 2 | `list_dir` core modules directory → 19 file names |\n| 3–9 | `view_file` × 7 (fast_context.ex, impact.ex, review.ex, onboard.ex, edit_context.ex, behaviour_trace.ex, tests_for.ex) |\n| 10–11 | `view_file` README.md × 2 (split across line ranges) |\n\n**Result:** 11 tool calls. 7 file reads consuming ~3,100 lines of source. No caller/callee graph. No linked tests. No related-code discovery.\n\n**Synapse approach** — graph queries only:\n\n| Step | Operation | What it returned |\n|---|---|---|\n| 1 | `synapse_fast_context` | Full dispatcher with all 27 registered tool modules, FastContext moduledoc, spec.md architecture pattern — all with callers/callees attached |\n| 2 | `synapse_onboard` | Layered reading order for the behaviour trace subsystem, key callees per hop, linked BDD tests, behavioural signals |\n| 3 | `synapse_explore_graph` (action `\"context\"`) ×3 (parallel) | Graph neighbourhood for impact, review, and onboard — callees, related chunks, spec.md cross-references |\n\n**Result:** 4 tool calls (3 parallelised). 0 file reads. Every result included caller/callee edges, related chunks, and linked tests that the manual approach never discovered.\n\n| Metric | Manual | Synapse |\n|---|---|---|\n| Tool calls | 11 | 4 |\n| File reads | 7 | 0 |\n| Lines of raw source in context | ~3,100 | 0 |\n| Caller/callee graph included | ❌ | ✅ |\n| Linked tests included | ❌ | ✅ |\n| Related chunks surfaced | ❌ | ✅ |\n\n---\n\n## Tool Surface\n\nUse **`ask_synapse`** as the default natural-language entry point for codebase\nquestions, edits, reviews, debugging, tests, repository/index administration,\nand capability discovery. Inspect `completion_state`; when it is\n`tool_call_required`, `clarification_required`, or `confirmation_required`, do\nnot treat the response as final—follow the first safe `next_tool_calls` entry\nor request the stated input. MCP guidance recommends this tool but cannot force\na client to select it.\n\nAll granular tools remain advertised and directly dispatchable during the\nstatic-additive compatibility stage. Use them for intentional known actions,\ndiagnostics, or a declared compatibility fallback. They are grouped below by\nworkflow stage and return structured data so agents spend tokens on reasoning,\nnot parsing.\n\n### 1. Understanding the Codebase\n- **`ask_synapse`** — Default natural-language entry point across the complete\n  Synapse capability surface; follow safe `next_tool_calls` for incomplete routes.\n- **`synapse_search_codebase`** — Search using semantic similarity, symbol lookups, or regex grep.\n  - Actions: `\"semantic\" | \"symbol\" | \"regex\"`\n  - **`regex` — always pass `repo_id`:** without it, the search scans all indexed repos, caps at 20 results, and returns a `synapse_warning` telling you to re-run with `repo_id`.\n  - **`regex` + `match_per_line: true`:** returns `[{repo_id, file, line_number, line_content}]` — ideal for locating specific function definitions.\n- **`synapse_explore_graph`** — Explore callers, callees, and context around a chunk.\n  - Actions: `\"callers\" | \"callees\" | \"context\"`\n  - **All three actions** accept `chunk_id` **or** `repo_id` + `symbol` **or** `repo_id` + `file_path` (+ optional `line`) — no prior lookup needed.\n  - One-call caller trace: `{action: \"callers\", repo_id: \"MY_REPO\", symbol: \"MyModule.fn/1\"}`\n  - One-call callee trace: `{action: \"callees\", repo_id: \"MY_REPO\", symbol: \"MyModule.fn/1\"}`\n- **`synapse_get_context`** — Advanced direct context gathering for known open-ended, editing-prep, or onboarding actions.\n  - Actions: `\"find\" | \"edit\" | \"explain\" | \"onboard\"`\n- **`synapse_inspect_files`** — Inspect file structures, read file ranges, or count lines in codebases.\n  - Actions: `\"read_files\" | \"read_chunk\" | \"count_lines\"`\n- **`synapse_codebase_insights`** — Detect languages, identify public APIs, scan interface contracts, build dependency graphs, surface refactoring opportunities, or retrieve consolidated repository overviews.\n  - Actions: `\"detect\" | \"public_api\" | \"contracts\" | \"dependencies\" | \"overview\" | \"refactor_opportunities\"`\n\n### 2. Making Changes Safely\n- **`synapse_modify_files`** — Edit source files atomically (overwrite/append/patch), run find-and-replace, or delete chunks. Integrates Trunk lint validation.\n  - Actions: `\"write_safely\" | \"find_and_replace\" | \"delete_chunk\"`\n- **`synapse_change_review`** — Analyse diffs, review change risks, and evaluate downstream blast-radius impact.\n  - Actions: `\"analyse_diff\" | \"review_diff\" | \"impact\"`\n- **`synapse_test_quality`** — Identify test coverage gaps, find feature/unit tests for a symbol, recommend test targets (both unit/integration and BDD features) with behaviour summaries, and configure Trunk.\n  - Actions: `\"coverage\" | \"find_tests\" | \"setup_trunk\" | \"recommend_test_targets\"`\n  - *Note on Nested Repositories (recommend_test_targets)*: By default, recommendations exclude nested repositories and git submodules (detected via `.git` or project markers). You can explicitly opt in to target a sub-repository by passing its directory path in the `path` parameter.\n- **`synapse_debug_trace`** — Trace ranked behavioral execution paths or map crash stack traces to code chunks.\n  - Actions: `\"trace_behaviour\" | \"resolve_stack\"`\n\n### 3. Knowledge & Repo Management\n- **`synapse_knowledge_cache`** — Manage learning query hits, save chunk summaries, and suggest docs needs.\n  - Actions: `\"learn\" | \"save_summary\" | \"suggest\"`\n- **`synapse_manage_repos`** — Register new repositories, manage lifecycle state, update exclude paths, unregister, or list all registered workspaces.\n  - Actions: `\"list\" | \"register\" | \"archive\" | \"restore\" | \"unregister\" | \"update_excludes\"`\n  - **Lifecycle management:** `list` responses include `lifecycle: \"active\" | \"archived\"`. Use `archive` for stale or merged worktrees so Synapse stops watching/re-indexing them while keeping existing graph data searchable; use `restore` when active indexing is needed again. Use `unregister` only for destructive graph removal.\n- **`synapse_indexer_control`** — Monitor indexing phase progress, health status, and trigger manual indexing.\n  - Actions: `\"status\" | \"trigger\" | \"health\"`\n- **`synapse_capability_manifest`** — Returns the structured manifest of live Synapse MCP tool capabilities.\n\n---\n\n## Key Design Principles\n\n- **Staged indexing** — a fast `quick_pass` makes the graph queryable within seconds; deeper semantic passes run in the background without blocking queries.\n- **Persistent across restarts** — the knowledge graph is written to SQLite and warmed back into ETS on startup; no cold-start delay after a server restart.\n- **Shared across IDEs** — in SSE mode, all connected IDEs share one index: one ingestion cost, universal benefit.\n- **Concurrent ingestion** — the indexing pipeline uses a worker pool scaled to CPU cores, saturating available hardware for maximum throughput on large monorepos.\n- **Smart exclusions** — build artefacts, dependency trees, caches, and framework outputs are excluded by default for Elixir, Python, JavaScript, and Node.js projects.\n\n---\n\n## Current Model\n\n- Workspaces opened in your IDE are automatically registered and indexed during the MCP connection handshake. Manual registration via `synapse_add_repo` is only required for external/secondary folders.\n- Indexing is staged so useful graph data appears before the full semantic pass completes.\n- Query tools report repo readiness so an agent can decide whether to wait, narrow scope, or continue with partial context.\n- **Cleaner graph answers (less symbol noise):** Elixir special-form noise is normalised and filtered (`when`, `->`, `<-`, `.`, `^`, `{}`, etc.), so `synapse_search_codebase` (symbol), `synapse_explore_graph` (context/callers/callees), and `synapse_get_context` (find) return cleaner structural results.\n- **FastContext richer outputs:** `synapse_fast_context` returns `structured_results`, `result_buckets` (primary implementation, callers/entry points, tests, related UI/observers), `index_health`, and stronger cache metadata (`cache_hit`, optional `cached_at`, `learn_hint`).\n- **FastContext implementation expansion:** thin dispatcher chunks are expanded by callee hops automatically, helping queries land on concrete implementation rather than only wrapper modules.\n- **Pre-edit planning:** `synapse_edit_context` builds an edit-readiness pack (call graph, likely tests, must-read files, behaviour boundaries, and risk-oriented guidance).\n- **Test discovery:** `synapse_tests_for` finds likely features, step definitions, tests, support files, and fixtures for a target symbol/chunk/query.\n- **Behaviour tracing:** `synapse_behaviour_trace` traces behavioural contracts from a target symbol/chunk, with runtime verification, entrypoint inference, and static signal extraction.\n- **Impact analysis:** `synapse_impact` evaluates downstream blast radius, identifying affected systems and deduplicating test plans.\n- **Code review:** `synapse_review` computes blast-radius risks, identifies blind spots, and surfaces contract warnings for diffs, files, or chunks.\n- **Onboarding:** `synapse_onboard` generates an ordered reading plan for a subsystem, grouped by architectural layers with estimated read times.\n- **Repo exclude management:** `synapse_update_repo_excludes` updates indexing exclusions with merge-or-replace behaviour.\n- **Repo lifecycle management:** `synapse_manage_repos` exposes manual `archive` and `restore` actions, and Synapse automatically archives clean Git worktrees whose branch work has already been merged into the parent checkout. Archived repositories keep their existing graph data searchable but are not restarted, watched, or re-indexed until restored.\n- **Status and diagnostics:** `synapse_status` reports watcher/indexer health, unresolved edge counts, query quality warnings, optional profile/vectorisation coverage, and high-traffic chunks needing summaries.\n- **Indexer and runtime hardening:** watcher reuse/re-subscribe behaviour is more robust; stale files and orphan noisy chunks are pruned; stale-chunk lazy reindexing is triggered from fast-context access paths.\n\n---\n\n## Behaviour Trace Examples\n\n### Automatic runtime verification (fully automatic)\nSet `runtime_verification` to `true` and Synapse will automatically derive observed symbols/events/tests from linked behavioural test artefacts.\n\n```json\n{\n  \"name\": \"synapse_behaviour_trace\",\n  \"arguments\": {\n    \"repo_id\": \"alpha\",\n    \"query\": \"CacheService.resolve/2\",\n    \"max_depth\": 6,\n    \"max_paths\": 3,\n    \"runtime_verification\": true\n  }\n}\n```\n\nResponse fields to inspect:\n- `paths[*].runtime_verification.observation_source` (`automatic_test_trace`, `manual_input`, `manual_and_automatic`, or `none`)\n- `paths[*].hops[*].verification.status` (`observed` or `inferred`)\n- `runtime_verification.auto_observed_symbol_count`\n- `runtime_verification.auto_observed_event_count`\n\n### Optional manual runtime overrides\nManual observation inputs are optional. If provided, they are merged with automatic evidence.\n\n```json\n{\n  \"name\": \"synapse_behaviour_trace\",\n  \"arguments\": {\n    \"chunk_id\": \"abc123\",\n    \"runtime_verification\": true,\n    \"observed_symbols\": [\"CacheService.resolve/2\"],\n    \"observed_events\": [\"telemetry_execute\"],\n    \"observed_tests\": [\"apps/core/test/features/cache_service_trace.feature\"]\n  }\n}\n```\n\n### Confidence and uncertainty reading\n- `confidence` reflects structural continuity, behaviour signals, entrypoint relevance, test linkage, and uncertainty penalties.\n- `uncertainty` explicitly flags inferred or weakly-supported path segments.\n- Treat low-confidence paths as hypotheses until runtime verification or stronger tests confirm them.\n\n## Semantic Diff Simulation (Shadow Graph)\n\nWhen an AI agent modifies code, finding out that a change breaks the build usually requires writing the file to disk, running the compiler, and waiting for the test suite. This slows down agent iteration loops significantly.\n\nSynapse solves this with **Semantic Diff Simulation**. By passing `dry_run: true` to `synapse_write_files_safely`, Synapse builds an ephemeral \"Shadow Graph\" of the proposed AST and compares it against the persisted index in milliseconds.\n\n- **Strict Rejection**: Compilation errors (e.g. arity mismatches, deleted symbols that break existing callers) are caught instantly via graph math and strictly rejected before any file is written.\n- **Contract Validation**: Non-fatal structural changes, like removing an emitted event or a state write, return as `contract_warnings`. This allows higher-level orchestrators to evaluate the risk of the change mathematically.\n- **Blast Radius Calculation**: Every simulation automatically traces callers to return a numeric `blast_radius`, allowing agents to gauge how broadly a change will impact the rest of the system.\n\nThis provides LLMs with a sub-10ms \"mathematical proof\" of diff safety without executing a single line of code.\n\n## Git Worktree Support & Virtual Worktree Overlay (VWO)\n\nWhen running parallel sub-agents or tasks, keeping files isolated via separate Git worktrees prevents file conflicts. However, indexing a new directory clone from scratch is slow, heavy, and wasteful.\n\nSynapse-MCP solves this with **Git Worktree Support** and the **Virtual Worktree Overlay (VWO)** system. When registering a repository root via `synapse_manage_repos` (action `\"register\"`), Synapse automatically detects if the root is a Git worktree.\n\n### Core Behaviour:\n1. **Delta Indexing:** Instead of a full workspace scan, Synapse runs `git status --porcelain` and `git diff` against the parent repository's current indexed commit. Only modified, added, or deleted files inside the worktree are indexed/updated, achieving near-instant indexing speed (< 50ms).\n2. **Virtual Worktree Overlay (VWO):** When querying a worktree's `repo_id` (via `synapse_get_context` or `synapse_search_codebase`):\n   - Chunks from modified or added files inside the worktree overlay take absolute precedence and shadow the parent repository's chunks.\n   - Chunks from deleted files inside the worktree overlay are completely suppressed (hidden).\n   - Unchanged files fall back seamlessly to the parent repository's indexed chunks.\n\nThis allows agents to spawn multiple parallel sub-agents in isolated worktrees while sharing the parent repository's warm cache and pre-built index, with zero overhead.\n\n### Stale worktree lifecycle management\n\nMerged or abandoned worktrees should be archived rather than left active. Archiving is intentionally non-destructive:\n- `lifecycle: \"active\"` means the repository can be watched, booted, and re-indexed.\n- `lifecycle: \"archived\"` means Synapse stops the repository indexer, excludes it from automatic boot/idle/manual re-index scheduling, and keeps its existing graph data searchable for historical lookup.\n- `archive` is the right action for stale CORTEX agent worktrees that should not be revived on restart.\n- `restore` reactivates a repository and restarts indexing when the worktree is needed again.\n- `unregister` remains the destructive removal path and deletes the repository's graph data.\nSynapse also performs conservative automatic stale-worktree archiving before boot,\nidle, query-start, and manual re-index scheduling. A worktree is auto-archived\nonly when it is a Git worktree, has a clean working tree, and its HEAD is already\nan ancestor of the parent checkout HEAD. Dirty, untracked, unmerged, or\nGit-error states remain active.\n\nWhen Synapse auto-archives a worktree, scoped `list`/status responses include\nadditive `stale_worktree` fields explaining that the worktree appears stale\nbecause the branch work was merged, plus guidance to restore only when active\nindexing is needed again.\n\nTypical manual stale-worktree cleanup flow:\n\n```json\n{ \"tool\": \"synapse_manage_repos\", \"input\": { \"action\": \"list\" } }\n```\n\nFind worktree `repo_id` values whose branches have been merged or whose directories are no longer in active use, then archive each one:\n\n```json\n{\n  \"tool\": \"synapse_manage_repos\",\n  \"input\": { \"action\": \"archive\", \"repo_id\": \"CORTEX-agent-example\" }\n}\n```\n\nIf a worktree needs to become live again:\n\n```json\n{\n  \"tool\": \"synapse_manage_repos\",\n  \"input\": { \"action\": \"restore\", \"repo_id\": \"CORTEX-agent-example\" }\n}\n```\n\nAutomatic archive is deliberately conservative. Use manual `archive` for abandoned\nworktrees that are not cleanly merge-detectable, and use `restore` when a\npreviously archived worktree needs active indexing again.\n\n## Code Outliner and JSON SmartCrusher\n\nTo conserve context tokens, Synapse-MCP provides two integrated compression features:\n\n### 1. AST-Based Code Outliner\nWhen inspecting code chunks or files via `synapse_inspect_files` (actions `\"read_chunk\"` and `\"read_files\"`), you can pass `format: \"outline\"` in the arguments.\nInstead of the full implementation, the outliner strips function and macro bodies down to `...` (or standard comment placeholders like `/* ... */` depending on the language strategy), keeping only function heads, docstrings, and type specs.\n\nOutliner configuration is file-based and loaded from `apps/synapse_core/priv/compressors/`. Currently supported:\n- **Elixir** (`elixir.json`): Uses `Sourceror` AST mapping to safely replace `do` blocks.\n- **Python** (`python.json`): Uses line indentation tracking to replace function bodies with `pass  # ...`.\n- **JavaScript & TypeScript** (`javascript.json`, `typescript.json`): Uses bracket matching to replace function block contents with `/* ... */`.\n\n*Example response content:*\n```elixir\ndef add(a, b) do\n  ...\nend\n```\n\n### 2. JSON SmartCrusher (ON by default)\nCompression is **enabled by default** on all tool responses. To opt out (e.g. for debugging), pass `compress_payload: false` in the arguments. The SmartCrusher minifies the returned JSON response:\n- **Key mapping:** Converts long verbose keys to shortened codes (e.g., `file_path` $\\rightarrow$ `fp`, `chunk_id` $\\rightarrow$ `cid`, `raw_source` $\\rightarrow$ `src`, `language` $\\rightarrow$ `lang`, `symbol` $\\rightarrow$ `sym`).\n- **Language shortening:** Converts verbose language names to extension-style short names (e.g., `elixir` $\\rightarrow$ `ex`, `python` $\\rightarrow$ `py`).\n- **Pruning:** Automatically strips empty lists (`[]`), empty maps (`{}`), and null/nil fields.\n- **Path relativisation:** Resolves absolute workspace paths to relative paths using the registered repository roots.\n- **Token savings:** 30-60% fewer response tokens with zero information loss.\n\nThis minification runs directly inside the tool `Dispatcher`, meaning both external JSON-RPC clients and embedded native Elixir callers (like Cortex's `SynapseMcpAdapter`) automatically receive optimised, token-dense payloads.\n\n---\n\n## CLI Orchestration (`synapse-cli`)\n\nThe `@myelixlabs/synapse-mcp` npm package is the recommended starting point for all users.\nIt is a zero-dependency Node.js CLI that handles the complete lifecycle: binary download,\ndevice sign-in, service management, OS autostart, IDE configuration, and the local dashboard.\n\n### Quick start\n\n```sh\nnpx @myelixlabs/synapse-mcp\n```\n\nOn first run this launches the full interactive wizard:\n\n1. **Downloads the launcher binary** from `downloads.synapse-mcp.dev` for your platform (macOS/Linux/Windows)\n2. **Signs you in** via a browser-based device code flow — no API keys needed\n3. **Starts the Synapse service** on `http://127.0.0.1:8585/mcp`\n4. **Registers OS autostart** (launchd on macOS, systemd user unit on Linux, Task Scheduler on Windows)\n5. **Detects and configures your IDEs** (Cursor, Antigravity, Claude, VS Code, Warp, Windsurf)\n6. **Opens the management dashboard** at `http://localhost:8686`\n\nOn subsequent runs the same command shows a status summary:\n\n```\n  Synapse MCP\n  Status     ●  running   (PID 34821)\n  Endpoint   http://127.0.0.1:8585/mcp\n  Indexer    ready\n  Repos      5\n  Autostart  ✔  launchd (dev.synapse-mcp)\n```\n\n### Installation via npm\n\n```sh\nnpm install -g @myelixlabs/synapse-mcp\n```\n\nThe `postinstall` script automatically runs `synapse-mcp install --quiet` to pre-download\nthe launcher binary. Manual install is not required.\n\n### Command reference\n\n```sh\nnpx @myelixlabs/synapse-mcp <command>\n```\n\n| Command | Description |\n|---------|-------------|\n| *(no command)* | Smart dispatch: setup wizard on first run, status on subsequent runs |\n| `install` | Full interactive setup wizard (download binary, sign in, configure IDEs) |\n| `start` | Start the Synapse service |\n| `stop` | Stop the Synapse service |\n| `restart` | Restart the Synapse service |\n| `status` | Rich status output (PID, endpoint, indexer, repos, autostart) |\n| `enable` | Register OS autostart (launchd / systemd / Task Scheduler) |\n| `disable` | Unregister OS autostart |\n| `auth` | Sign in via device code flow, or show current account status |\n| `auth refresh` | Re-fetch latest licence info (tier, status, token) |\n| `auth status` | Show account status without starting sign-in |\n| `logout` | Remove local credentials |\n| `repos list` | List all registered repositories with lifecycle state |\n| `repos add <path>` | Register a repository at the given path |\n| `repos archive <id>` | Archive a repository (stops indexing, keeps graph data) |\n| `repos restore <id>` | Restore an archived repository |\n| `repos remove <id>` | Unregister and delete graph data (destructive, confirms first) |\n| `repos reindex <id>` | Trigger a fresh full index pass |\n| `ui` | Start the management dashboard and open it in the browser |\n| `ui stop` | Stop the background dashboard server |\n| `upgrade` | Re-download the launcher binary from downloads.synapse-mcp.dev |\n| `version` | Print the CLI shim version |\n\n### Ports\n\n| Service | Default port | Override |\n|---------|-------------|---------|\n| Synapse MCP (Elixir SSE/HTTP) | **8585** | `SYNAPSE_PORT` env var |\n| Management dashboard (Node.js) | **8686** | `SYNAPSE_DASHBOARD_PORT` env var |\n\nThe Synapse service exposes both transport modes on the same port:\n- `/mcp` — Streamable HTTP (recommended, default)\n- `/sse` — Server-Sent Events (legacy SSE clients)\n\nConfigure your IDE with `{ \"synapse\": { \"serverUrl\": \"http://127.0.0.1:8585/mcp\" } }`.\n\n### Authentication\n\nSign-in uses the OAuth 2.0 device code flow — no passwords or API keys stored locally.\n\n1. CLI prints a URL (`https://synapse-mcp.dev/device`) and a short code (`WXYZ-4821`)\n2. You open the URL in a browser and enter the code\n3. CLI polls every 3 seconds and saves credentials on success:\n   - `~/.config/synapse-mcp/token.jwt` — 7-day Ed25519 JWT\n   - `~/.config/synapse-mcp/credentials.json` — `{ \"license_key\": \"sk_live_...\" }` (mode `0600`)\n\nThe **Rust launcher** (not the Node CLI or Elixir runtime) is the authoritative\nenforcement path: it verifies the cached JWT offline, refreshes via\n`POST /api/v1/license/renew` on a daily background heartbeat (and on demand via\n`synapse-mcp auth refresh`), and terminates the MCP\nruntime on repeated hard license failures. The Elixir runtime writes\n\nAfter upgrading (e.g. Free → Pro), refresh your local entitlement in one of three\nways: open `synapse://billing/complete` in the Synapse app, press **Refresh**\nin the **User** tab of the local Synapse Dashboard, or run\n`synapse-mcp auth refresh` in your terminal.\n\nFree tier requires a sign-up with an email. Upgrade to Pro at `https://synapse-mcp.dev/dashboard`.\n\n### OS Autostart\n\nThe CLI writes and activates a **user-level** (not system-level) service unit:\n\n| Platform | Mechanism | File |\n|----------|-----------|------|\n| macOS | launchd | `~/Library/LaunchAgents/dev.synapse-mcp.plist` |\n| Linux | systemd user unit | `~/.config/systemd/user/synapse-mcp.service` |\n| Windows | Task Scheduler | Task name `SynapseMCP` |\n\nAll units restart the service on crash (`KeepAlive`/`Restart=always`) and launch at login\nwithout requiring root or admin privileges.\n\n### Management Dashboard\n\nThe dashboard is a local web UI served by the Node.js CLI at `http://localhost:8686`.\n\n```sh\n# Start the dashboard and open in your browser\nnpx @myelixlabs/synapse-mcp ui\n\n# Stop the background dashboard server\nnpx @myelixlabs/synapse-mcp ui stop\n```\n\nIf a dashboard is already running when you invoke `ui`, the CLI detects the conflict and prompts:\n\n```\n⚠  Dashboard already running  (PID 12345)  →  http://localhost:8686\n\n  [1]  Open the existing dashboard in your browser\n  [2]  Kill the existing instance and start a fresh one\n  [3]  Cancel\n```\n\n**Tabs:**\n- **Overview** — service status, metrics (repos, chunks, cache hit rate, ETS memory), one-click copy MCP config snippet\n- **Repos** — browse, register, archive, restore, and remove repositories; per-repo index progress bars\n- **Indexer** — live phase progress (quick_pass → deep_dive_1 → deep_dive_2), health stats, trigger manual reindex\n- **Account** — licence tier, expiry, upgrade CTA → `synapse-mcp.dev/dashboard`\n- **Logs** — live streaming log output from the Synapse service with keyword filter\n\nThe dashboard SPA is shipped pre-built inside the npm package at `lib/ui-dist/`\n(vanilla HTML/CSS/JS — no build step required). It degrades gracefully when the\nElixir service is not running — cards show \"Unreachable\" and metrics show `—`.\n\n### IDE Auto-Detection\n\nThe CLI detects and configures MCP servers for the following IDEs automatically:\n\n| IDE | Config file |\n|-----|-------------|\n| Cursor | `~/.cursor/mcp.json` |\n| Antigravity | `~/.antigravity/mcp.json` |\n| Claude Code | `~/.claude.json`, `~/.claude/mcp.json`, `./.mcp.json` |\n| VS Code | `~/.config/Code/User/mcp.json` (Linux) / `AppData/Code/User/mcp.json` (Windows) |\n| Windsurf | `~/.codeium/windsurf/mcp_config.json` |\n| Warp | `~/.warp/mcp.json` |\n| Codex | `~/.codex/config.toml` (TOML format) |\n\nAll JSON-based IDEs receive:\n```json\n{ \"mcpServers\": { \"synapse\": { \"serverUrl\": \"http://127.0.0.1:8585/sse\" } } }\n```\n\n### Running Synapse — Dev Mode vs Production Mode\n\nSynapse has two launch modes with different purposes but **unified management**.\nRegardless of how the server was started, `synapse-mcp status`, `stop`, and `start`\nall work the same way.\n\n| | Dev Mode | Production Mode |\n|---|---|---|\n| **When to use** | Developing Synapse itself | End-users, CI, production |\n| **Start command** | `./bin/synapse_mcp --http --replace` | `synapse-mcp start` |\n| **Binary** | Source code via Mix (`elixir -S mix run`) | Burrito-packed binary (`~/.synapse-mcp/synapse-mcp`) |\n| **Lifecycle** | Foreground, live logs, `q` to quit | Daemon, PID file, detached |\n| **Pre-flight** | `mix deps.get` → `mix compile --force` → `mix ecto.migrate` | None (self-contained) |\n| **Default port** | `8585` (via `SYNAPSE_PORT`) | `8585` |\n| **PID file** | None (detected via port probe) | `~/.synapse-mcp/synapse.pid` |\n\n#### Unified management\n\nThe CLI uses **port-based discovery** as a fallback when no PID file exists. This means\nall management commands work identically regardless of how the server was started:\n\n```sh\n# These work whether the server was started in dev or production mode:\nsynapse-mcp status    # → detects running server via PID file or port probe\nsynapse-mcp stop      # → finds PID via file or lsof, sends SIGTERM → SIGKILL\nsynapse-mcp start     # → checks port first, won't double-spawn\n```\n\nStatus output adapts to reflect the launch mode:\n\n```\n# Dev-mode server (no PID file, detected via port probe):\n  Synapse MCP\n  Status     ●  running   (external process)\n  Endpoint   http://127.0.0.1:8585/mcp\n\n# Production server (managed via PID file):\n  Synapse MCP\n  Status     ●  running   (PID 34821)\n  Endpoint   http://127.0.0.1:8585/mcp\n```\n\n#### Dev mode — developing Synapse\n\nUse this when working on the Synapse-MCP codebase itself:\n\n```sh\ncd /path/to/SYNAPSE-MCP\n\n# Start the dev server (compiles, migrates, runs in foreground)\n./bin/synapse_mcp --http --replace\n# → starts on http://127.0.0.1:8585/mcp\n# → --replace kills any existing server on the same port first\n# → press q + Enter to stop, or Ctrl-C to interrupt\n```\n\nThe `--replace` flag is important: it finds and kills any existing Synapse process on the\nport before starting a fresh one, preventing stale-code issues during development.\n\n#### Production mode — the Burrito binary\n\nThe binary is installed at `~/.synapse-mcp/synapse-mcp` after running `synapse-mcp install`\nor `npx @myelixlabs/synapse-mcp`. The CLI manages it as a background daemon:\n\n```sh\n# Start the binary-managed service\nsynapse-mcp start\n# → spawns ~/.synapse-mcp/synapse-mcp --http --port 8585\n# → polls http://127.0.0.1:8585/mcp until ready\n# → writes ~/.synapse-mcp/synapse.pid\n\n# Test every command:\nsynapse-mcp status\nsynapse-mcp repos list\nsynapse-mcp repos add --path /path/to/project\nsynapse-mcp ui          # opens http://localhost:8686\nsynapse-mcp auth        # device code flow sign-in\nsynapse-mcp auth refresh # re-fetch latest licence entitlement\nsynapse-mcp enable      # register OS autostart\nsynapse-mcp upgrade     # re-download launcher binary\n\n# Stop when done:\nsynapse-mcp stop\n```\n\n---\n\n#### Auth — skip device flow for local testing\n\nThe auth device flow hits `https://api.synapse-mcp.dev`. To bypass it and test the CLI\nwithout network auth, create a stub credentials file:\n\n```sh\nmkdir -p ~/.config/synapse-mcp\n\n# Minimal credentials stub (bypasses the sign-in step in the wizard)\necho '{\"license_key\":\"sk_dev_local\",\"tier\":\"pro\"}' > ~/.config/synapse-mcp/credentials.json\nchmod 600 ~/.config/synapse-mcp/credentials.json\n\n# Fake JWT so the wizard skips the sign-in step entirely\necho 'dev.stub.token' > ~/.config/synapse-mcp/token.jwt\n```\n\nFor the real device-code flow against a fully local auth backend (not the\nstub above) — including running `myelixlabs_umbrella` locally, signing up,\nand avoiding the dev-vs-packaged-binary pitfall — see\n[`docs/local-dev-setup.md`](docs/local-dev-setup.md).\n\n---\n\n#### Dashboard UI only (no Elixir server needed)\n\nThe dashboard degrades gracefully — service cards show \"Unreachable\" and metrics show `—`\nif the Elixir service is not running. You can inspect and develop the UI without a live server:\n\n```sh\nsynapse-mcp ui\n# → http://localhost:8686 opens immediately\n# → serves lib/ui-dist/ (vanilla HTML/CSS/JS, no build step)\n```\n\n---\n\n#### BDD tests — no binary, no network, full coverage\n\nThe CLI has a full Cucumber BDD suite (~700+ steps) covering every command. All external\ndependencies (OS calls, process.kill, browser open, service probes) are injected —\nno real network or OS interaction occurs.\n\n```sh\ncd /path/to/SYNAPSE-MCP/synapse-cli\nnpm install\n\n# Full suite — all scenarios stubbed, runs anywhere, no live service needed\nnpm test\n\n# Or explicitly:\nnpx cucumber-js --tags \"not @wip\"\n\n# View the HTML test report\nopen test-reports/cucumber-report.html\n```\n\n---\n\n#### System diagram: what talks to what\n\n```\nBrowser (:8686)  →  Express server.js  →  MCP client (:8585)  →  Elixir /api/*\n                                        ↘  service.js  (spawn / stop / port probe / pid file)\n                                        ↘  service-os.js  (launchd / systemd / schtasks)\n                                        ↘  auth.js  (~/.config/synapse-mcp/)\n```\n\nThe single env var that wires everything together is **`SYNAPSE_PORT`**.\nLeave it unset for the default (`8585`), or set it to override.\n\n\n### Environment variable reference\n\n| Variable | Default | Purpose |\n|----------|---------|---------|\n| `SYNAPSE_PORT` | `8585` | Synapse service port |\n| `SYNAPSE_DASHBOARD_PORT` | `8686` | Dashboard server port |\n| `SYNAPSE_MCP_INSTALL_DIR` | `~/.synapse-mcp` | Launcher binary location |\n| `XDG_CONFIG_HOME` | `~/.config` | Config/credentials root |\n| `SYNAPSE_DATA_DIR` | `~/.synapse-mcp/data` | SQLite database directory |\n| `SYNAPSE_MCP_TELEMETRY` | `1` | Set to `0` to disable usage telemetry served at `GET /internal/telemetry` |\n| `SYNAPSE_DB_PATH` | — | Full path to SQLite file (overrides `SYNAPSE_DATA_DIR`) |\n\n---\n\n## Prerequisites\n\n### Trunk CLI — polyglot lint validation for write-safe operations (optional)\n\n\n[Trunk](https://trunk.io) is a polyglot linter orchestrator. It wraps existing tools like\n`shellcheck`, `prettier`, `markdownlint`, `yamllint`, and more behind a single binary and\nconfiguration file (`.trunk/trunk.yaml`). You define which linters to enable once; Trunk\ninstalls and runs them consistently across every machine and CI environment.\n\n#### What Trunk does in Synapse\n\n`synapse_write_files_safely` and `synapse_sed` use Trunk as a validation gate. Every write\npasses through this sequence:\n\n1. **Write** the new content to disk (or apply the sed replacement).\n2. **Validate** the modified file(s) by calling `trunk check` against the paths.\n3. If Trunk exits clean → **commit** the write and trigger immediate re-indexing.\n4. If Trunk reports violations → **rollback**: the file is restored to its original content\n   from an in-memory backup. Nothing broken is left on disk.\n\nThe agent receives a structured **Diagnostic Map** on failure:\n\n```json\n{\n  \"status\": \"error\",\n  \"type\": \"lint_violation\",\n  \"message\": \"Your edit introduced lint errors. The file has not been saved.\",\n  \"action\": \"Please correct the logic and retry the write.\",\n  \"details\": [\n    {\n      \"file\": \"bin/my_script\",\n      \"line\": \"6\",\n      \"column\": \"6\",\n      \"linter\": \"shellcheck\",\n      \"message\": \"SC2086: Double quote to prevent globbing and word splitting\"\n    }\n  ]\n}\n```\n\nThe LLM reads the diagnostic, corrects the content, and retries — completing the loop\nwithout any human intervention or broken state on disk.\n\n#### Why this matters\n\nWithout lint validation, an agent can silently commit a shell script that breaks CI, a\nYAML file with invalid indentation, or a Markdown document with formatting violations.\nWith the write-safe layer, those classes of error never land on disk. The rollback is\natomic — it happens in-process before the write is finalised — so there is no partial\nstate to clean up.\n\nLint results for repeated content are cached by content hash in ETS, so re-running Trunk\non the same file after a no-op change costs nothing.\n\n#### What linters are enabled\n\nDefined in `.trunk/trunk.yaml`:\n\n| Linter | Coverage |\n|---|---|\n| `shellcheck` | Shell script correctness |\n| `shfmt` | Shell script formatting |\n| `prettier` | JS, TS, CSS, HTML, JSON, Markdown |\n| `markdownlint` | Markdown structure and style |\n| `yamllint` | YAML formatting and structure |\n| `checkov` | Infrastructure-as-code security scanning |\n| `trufflehog` | Secret / credential leak detection |\n| `grype` | Dependency vulnerability scanning |\n| `osv-scanner` | Open source vulnerability database |\n| `git-diff-check` | Whitespace and conflict markers |\n\n#### Graceful degradation\n\nIf `trunk` is not in PATH, Synapse degrades safely:\n- Writes proceed unconditionally.\n- Responses include `\"lint_applied\": false`.\n- A warning is logged at boot: `trunk not found in PATH. Write-safe linting is disabled. Run bin/install to enable.`\n\nNo functionality is lost except the lint gate.\n\n#### Installing Trunk\n\nRun the included install script (idempotent — safe to run repeatedly):\n\n```sh\nbash bin/install\n```\n\nThe script:\n1. Checks whether `trunk` is already installed and skips download if so.\n2. Installs the Trunk CLI via the official installer.\n3. Runs `trunk install` to download the linters defined in `.trunk/trunk.yaml`.\n\nOr install manually:\n\n```sh\ncurl https://get.trunk.io -fsSL | bash\ntrunk install\n```\n\nVerify:\n\n```sh\ntrunk --version   # e.g. 1.25.0\n```\n\n---\n\n## Free vs Pro Tiers\n\nSynapse-MCP ships in two tiers. The split is enforced at **compile time**, not just at runtime, so the Free binary physically cannot contain Pro bytecodes.\n\nFor the canonical description of entitlement, artifact selection, renewal, and\nknown lifecycle limitations, see [`docs/licensing.md`](docs/licensing.md). For\ncomponent and version boundaries, start with [`docs/README.md`](docs/README.md).\n\n### How the compilation model works\n\nThe umbrella has three apps:\n\n| App | Contains | Included in Free binary | Included in Pro binary |\n|---|---|---|---|\n| `synapse_core` | Graph engine, ETS store, indexer, SQLite | ✅ always | ✅ always |\n| `synapse_mcp` | MCP transport, dispatcher, Free tools, Pro stubs | ✅ always | ✅ always |\n| `synapse_pro` | Pro tool implementations (ChangeReview, TestQuality, ExploreGraph, CodebaseInsights, KnowledgeCache, DebugTrace) | ❌ excluded | ✅ included |\n\nThe Burrito release target in `mix.exs` controls this:\n\n```elixir\nreleases: [\n  synapse_mcp: [\n    applications: [\n      synapse_mcp: :permanent,\n      synapse_core: :permanent\n      # synapse_pro is deliberately absent — Free release only\n    ],\n    ...\n  ]\n]\n```\n\nWhen `synapse_pro` is absent from the release, every Pro tool name registered in the dispatcher falls through to `SynapseMcp.Tools.ProStubs`, which returns a structured upgrade prompt instead of a result. The Pro bytecode is never assembled into the binary and cannot be reverse-engineered from it.\n\n### Pro tools — how stubs work\n\nWhen a Free-tier user calls a Pro tool (e.g. `synapse_change_review`), the dispatcher detects that `SynapsePro.*` modules are not loaded and routes to `ProStubs.call/2`. The response is:\n\n```json\n{\n  \"error\": \"pro_feature\",\n  \"tool\": \"synapse_change_review\",\n  \"message\": \"This tool requires Synapse Pro. Upgrade at ...\",\n  \"upgrade_url\": \"...\"\n}\n```\n\nThis happens entirely inside the Free binary — no network call is made.\n\n### Dev environment\n\nIn development all three umbrella apps compile together. `synapse_pro` is always available. The dispatcher operates in **Pro mode by default**.\n\n```sh\n# Start with full Pro features (default in dev)\nbin/synapse_mcp --http\n\n# Force the Free tier locally — Pro tools return upgrade stubs\nbin/synapse_mcp --http --free\n```\n\nThe `--free` flag sets `SYNAPSE_TIER=free` which the dispatcher checks at tool-list build time to exclude Pro tool definitions from the `tools/list` response, even though the Pro modules are compiled and present.\n\n### Test environment\n\nTests run with all three apps compiled (`MIX_ENV=test` compiles the full umbrella). Pro tools are available by default. To test Free-tier behaviour, set `SYNAPSE_TIER=free` in the test process:\n\n```elixir\n# In a BDD step or ExUnit test\nSystem.put_env(\"SYNAPSE_TIER\", \"free\")\n# ...test stub responses...\nSystem.delete_env(\"SYNAPSE_TIER\")\n```\n\nThe BDD suite `pro_tier_gating.feature` covers this explicitly — it verifies that Pro tool names return upgrade errors in Free mode and full results in Pro mode.\n\nRun the full test suite including tier-gating tests:\n\n```sh\nmix test --warnings-as-errors\n# or with coverage:\nmix test --cover --warnings-as-errors\n```\n\n### Production — Free binary\n\nThe Free production binary is assembled by Burrito from the `synapse_mcp` release target, which excludes `synapse_pro`. The resulting binary is a self-contained executable for macOS (Intel + ARM), Linux, and Windows.\n\n```sh\n# Build the Free binary for all platforms\nMIX_ENV=prod mix release synapse_mcp\n\n# Or via Burrito cross-compilation\nMIX_ENV=prod mix burrito.build\n```\n\nThe binary is fully standalone — it embeds the Erlang runtime and has no external dependencies except SQLite (linked at build time). Users run it directly:\n\n```sh\n# Start as persistent HTTP server (production recommended)\n./synapse_mcp_macos_arm --http\n\n# Start as stdio process (IDE-managed)\n./synapse_mcp_macos_arm\n```\n\n### Production — Pro binary\n\nThe Pro build includes `synapse_pro` in the release applications list and is\npublished as a complete encrypted `base_pro` runtime artifact. The shared Rust\nlauncher verifies the signed entitlement and selects `base_pro`; it does not\npatch Pro bytecode into the Free `base` runtime.\n\nRuntime and launcher updates are separate mechanisms. See\n[`docs/auto-update.md`](docs/auto-update.md) for their scheduling, restart, and\nrollback behavior.\n\n### Environment variable reference\n\n| Variable | Values | Effect |\n|---|---|---|\n| `SYNAPSE_TIER` | `free` \\| `pro` (default) | Forces tier at runtime. In dev, overrides the compiled presence of `synapse_pro`. |\n| `SYNAPSE_TRANSPORT` | `streamable-http` \\| `sse` \\| `stdio` | Selects MCP transport. Set automatically by `--http` / `--sse` flags. |\n| `SYNAPSE_PORT` | integer (default `8585`) | HTTP/SSE server port. |\n\n---\n\n## Developer Installation Guide\n\nTo develop and run Synapse-MCP, you need the following system dependencies installed:\n- **Erlang**: 29.0.5\n- **Elixir**: 1.20.1 (OTP 29)\n- **SQLite3** (on macOS, you can run `brew install sqlite`)\n- A C/C++ compiler (for compiling SQLite NIFs)\n\nWe recommend using [asdf](https://asdf-vm.com/) for version management. Once asdf is installed, run:\n```sh\nasdf plugin add erlang\nasdf plugin add elixir\nasdf install\n```\n\n## Running the Server Locally\n\n### One-time setup\nRun this once before starting the server for the first time (installs dependencies and creates the SQLite database):\n\n```sh\ncd /path/to/SYNAPSE-MCP\nmix deps.get && mix compile && mix ecto.migrate\n```\n\nBut you can just run the convenience script; `bin/synapse_mcp` handles `mix deps.get`, `mix compile` and `mix ecto.migrate` automatically on every start. \n---\n\n### Mode A — Persistent Streamable HTTP server (recommended remote transport)\n\nRun one server process that all IDEs share. MCP clients connect to the Streamable HTTP endpoint at `http://127.0.0.1:8585/mcp`.\n\n> If you make changes to the server and want to test in your IDE, restart it and wait for the indexer to warm up before reconnecting.\n\n```sh\nbin/synapse_mcp --http\n```\n\nThe equivalent explicit transport form is:\n\n```sh\nbin/synapse_mcp --transport streamable-http\n```\n\nTo freshen the index on restart, pass `--reindex` to clear the database and force a full re-parse:\n\n```sh\nbin/synapse_mcp --http --reindex\n```\n\nThe `--replace` flag kills any existing Synapse process on the same port before starting:\n\n```sh\nbin/synapse_mcp --http --replace\n```\n\nThe server starts on `http://127.0.0.1:8585`. Keep this terminal open.\nThe `--http` flag sets `SYNAPSE_TRANSPORT=streamable-http` which picks up the HTTP config from `dev.exs`.\n\n**Why this is better:**\n- One process, one index — all IDEs share the same knowledge graph.\n- No cold-start delay per IDE connection.\n- Restarts are under your control.\n- Uses the current MCP Streamable HTTP transport instead of the older endpoint-event SSE flow.\n\n#### Connecting IDEs in Streamable HTTP mode\n\nUse `http://127.0.0.1:8585/mcp` as the remote MCP URL. Client configuration keys vary by IDE, but the transport should be HTTP or Streamable HTTP rather than SSE.\n\nExample MCP client configuration:\n\n```json\n{\n  \"mcpServers\": {\n    \"synapse\": {\n      \"type\": \"http\",\n      \"url\": \"http://127.0.0.1:8585/mcp\"\n    }\n  }\n}\n```\n\nIf your client exposes a dedicated Streamable HTTP transport name, prefer it:\n\n```json\n{\n  \"mcpServers\": {\n    \"synapse\": {\n      \"type\": \"streamable-http\",\n      \"url\": \"http://127.0.0.1:8585/mcp\"\n    }\n  }\n}\n```\n\n#### Legacy SSE compatibility\n\nLegacy SSE remains available for clients that have not moved to Streamable HTTP yet. Start the same persistent server with:\n\n```sh\nbin/synapse_mcp --sse\n```\n\nLegacy clients should continue using `http://127.0.0.1:8585/sse`. This path preserves the older MCP HTTP+SSE endpoint-event model:\n\n```text\nGET /sse\nevent: endpoint\ndata: http://localhost:8585/message?sessionId=...\n\nPOST /message?sessionId=...\n```\n\nExample legacy SSE configuration:\n\n```json\n{\n  \"mcpServers\": {\n    \"synapse\": {\n      \"type\": \"sse\",\n      \"url\": \"http://127.0.0.1:8585/sse\"\n    }\n  }\n}\n```\n\nKeep using this only for compatibility. New remote client configuration should target `/mcp`.\n\n---\n\n### Mode B — Per-process stdio (IDE-managed)\n\nEach IDE spawns its own server process over stdin/stdout. This is slightly less efficient (separate index per client) but requires no persistent terminal.\nThis mode is preserved for local/native process integrations, including products that start Synapse as a child process instead of connecting over remote HTTP.\n\n```sh\nbin/synapse_mcp\n```\n\n**Claude Desktop** (`~/Library/Application Support/Claude/claude_desktop_config.json`):\n```json\n{\n  \"mcpServers\": {\n    \"synapse\": {\n      \"command\": \"/absolute/path/to/SYNAPSE-MCP/bin/synapse_mcp\",\n      \"cwd\": \"/absolute/path/to/SYNAPSE-MCP\"\n    }\n  }\n}\n```\n\n**Cursor** (`.cursor/mcp.json`):\n```json\n{\n  \"mcpServers\": {\n    \"synapse\": {\n      \"command\": \"/absolute/path/to/SYNAPSE-MCP/bin/synapse_mcp\",\n      \"cwd\": \"/absolute/path/to/SYNAPSE-MCP\"\n    }\n  }\n}\n```\n\n**Windsurf** — MCP settings → add server → type **stdio**:\n```\ncommand: /absolute/path/to/SYNAPSE-MCP/bin/synapse_mcp\n```\n\n**Warp** (`mcp.json` in project root, copy from `mcp.json.example`):\n```json\n{\n  \"synapse\": {\n    \"command\": \"/absolute/path/to/SYNAPSE-MCP/bin/synapse_mcp\",\n    \"cwd\": \"/absolute/path/to/SYNAPSE-MCP\",\n    \"env\": {\n      \"ASDF_ERLANG_VERSION\": \"29.0.5\",\n      \"ASDF_ELIXIR_VERSION\": \"1.20.1-otp-29\"\n    }\n  }\n}\n```\n\n> `mcp.json` is gitignored. Copy `mcp.json.example` to `mcp.json` and fill in your absolute path.\n> Never configure the MCP client to run `mix compile` or `mix ecto.migrate` on connection.\n\n---\n\n### Verifying connectivity\n\nIn any terminal while the server is running (`--http`, `--sse`, or stdio):\n\n```sh\n# Inspector (works with stdin/stdout process)\nnpx @modelcontextprotocol/inspector /absolute/path/to/SYNAPSE-MCP/bin/synapse_mcp\n\n# Quick Streamable HTTP smoke test (when running --http)\ncurl -sS http://127.0.0.1:8585/mcp \\\n  -H 'content-type: application/json' \\\n  -H 'accept: application/json, text/event-stream' \\\n  -d '{\n    \"jsonrpc\": \"2.0\",\n    \"id\": 1,\n    \"method\": \"initialize\",\n    \"params\": {\n      \"protocolVersion\": \"2025-03-26\",\n      \"capabilities\": {},\n      \"clientInfo\": {\"name\": \"curl\", \"version\": \"0.1\"}\n    }\n  }'\n```\n\nExpected response:\n\n```json\n{\n  \"jsonrpc\": \"2.0\",\n  \"id\": 1,\n  \"result\": {\n    \"protocolVersion\": \"2025-03-26\",\n    \"capabilities\": {\n      \"tools\": {\n        \"listChanged\": false\n      }\n    },\n    \"serverInfo\": {\n      \"name\": \"synapse-mcp\",\n      \"version\": \"3.0.0\"\n    }\n  }\n}\n```\n\nFor legacy SSE compatibility checks:\n\n```sh\ncurl -N http://127.0.0.1:8585/sse\n```\n\nManual tool sequence once connected (any IDE):\n1. `ask_synapse` with the natural-language objective — default entry point\n2. Follow its safe `next_tool_calls` when the response is not complete\n3. Use a granular `synapse_*` action directly only for an intentional known\n   action or declared compatibility fallback\n\n\n## Runtime repo workflow\nThe default development config does not register a permanent repo. A typical client workflow is:\n\n1. Call `tools/list` if the agent has not seen the tool catalogue yet.\n2. Call `synapse_indexer_control` with action `\"health\"` to confirm transport health.\n3. Workspaces are automatically registered via the MCP handshake (or manually via `synapse_manage_repos` with action `\"register\"`).\n4. **Call `ask_synapse` first** with the natural-language objective and explicit inputs. Follow safe returned `next_tool_calls` before using a granular fallback.\n5. Call `synapse_explore_graph` with action `\"context\"` when you already know a specific file, line, symbol, or chunk.\n6. Call `synapse_inspect_files` with action `\"read_chunk\"` before modifying specific implementation details.\n7. **Use `synapse_inspect_files` with action `\"read_files\"` to explore directory structures.** Passing a directory path (e.g., `lib/`) returns its indexed children. **Do not use shell commands like `ls` or `find` to traverse the codebase.**\n8. During heavy indexing pressure, pass `repo_id` and `path` to `ask_synapse` — it narrows scope automatically. Fall back to `synapse_search_codebase` with action `\"symbol\"` / `\"regex\"` only when `ask_synapse` returns a suggested retry.\n\n## Advanced Direct Deep Search (`synapse_get_context`)\n`synapse_get_context` with action `\"find\"` remains available as an advanced\ndirect action and compatibility fallback. For ordinary requests,\n`ask_synapse` selects the appropriate capability. When `find` is selected, it\navoids multiple turns calling `search` → `read` → `callers` → `read` by doing\nthe heavy lifting in parallel:\n\n- Executes massive concurrent **semantic, exact, and fuzzy lookups**.\n- Instantly traverses the in-memory knowledge graph to pull **direct callers, callees, and related chunks**.\n- Expands thin dispatcher wrappers to reach concrete implementation chunks automatically.\n- Ranks results using a **Golden Score** heuristic (semantic relevance + graph centrality + usage signals).\n- Returns a single, highly dense, **LLM-friendly Markdown payload** designed to maximize context while minimizing token usage.\n- Also returns machine-friendly fields: `structured_results`, `result_buckets`, and `index_health`.\n\n## Staged indexing\nEach repo moves through named phases:\n\n- `quick_pass`: file discovery, chunk extraction, tags, symbols, and cheap graph edges\n- `deep_dive_1`: the first semantic enrichment pass\n- `deep_dive_2`: the later semantic enrichment pass\n- `full`: run the complete staged sequence\n- `x_repo`: cross-repo link pass — resolves unresolved edges **between** repos\n\n`synapse_index` accepts repo-wide `mode` values:\n\n- `quick_pass`\n- `deep_dive_1`\n- `deep_dive_2`\n- `full`\n- `x_repo` *(omit `repo_id` — runs across all registered repos)*\n\nThe `x_repo` pass scans every unresolved edge in the graph (`to_chunk_id: null`) and matches `to_symbol` against the global symbol index across all repos. Where an unambiguous match exists, the edge is resolved in-place — callee traversal in `fast_context` then works across repo boundaries automatically. Run it after all repos have completed their `quick_pass`.\n\nStatus-aware responses expose:\n\n- `status`\n- `current_phase`\n- per-phase `completed_files`, `total_files`, and `pending_files`\n- `quick_pass_ready`\n- `embeddings_partial`\n- `discovered_file_count`\n- `is_provisional`\n\nWhen a search or lookup is not explicitly scoped to a repo, Synapse infers repo readiness from the returned chunks and includes either `repo_status` or `repo_statuses`.\n\n## Indexing workflow and trigger map\n\nUnderstanding *when* and *why* the Indexer runs saves you from confusing repeated quick-pass completions in the logs. Every re-scan flows through `{:prepare_reindex, mode}`. Here is every path that fires one:\n\n### 1. Boot (server start)\nOn `init/1` the Indexer reads `boot_index_mode` from application config (default `:full` in `dev.exs`, `:quick_pass` or `:full` depending on environment). It schedules `{:prepare_reindex, mode}` within 1 ms via `handle_continue(:full_index)`.\n\n```\ninit/1\n  └── handle_continue(:full_index)\n        └── {:prepare_reindex, boot_index_mode}   ← first quick_pass\n```\n\nThe `boot_index_mode` value determines what happens:\n- `:quick_pass` — only structure/symbols/edges are built; **no embeddings**. Fast, queryable within seconds.\n- `:full` — runs `quick_pass`, `deep_dive_1`, and `deep_dive_2` all in sequence.\n\n### 2. Boot follow-up (automatic deeper pass after quick_pass)\n\nIf `boot_index_mode: :quick_pass` and `boot_followup_mode: :full` (the **dev.exs default**), once the quick_pass drains to `:done`, the Indexer schedules a second full-pass automatically:\n\n```\nquick_pass complete\n  └── maybe_schedule_boot_followup_reindex/1\n        └── {:prepare_reindex, :full}              ← deep follow-up\n```\n\nThis is why you often see a quick_pass immediately followed by another full scan in dev — it is intentional. The pattern gives instant structural readiness then catches up on embeddings in the background.\n\nConfig keys:\n```elixir\n# config/dev.exs\nconfig :synapse_core,\n  boot_index_mode: :quick_pass,\n  boot_followup_mode: :full\n```\n\n### 3. Idle follow-up (periodic coverage catch-up)\n\nThe Indexer fires an `:idle_maintenance_tick` on a configurable interval. When it does, it checks four conditions:\n1. The Indexer is idle with no active tasks.\n2. Embedding coverage is below `idle_followup_coverage_threshold_percent` (default 95%).\n3. At least `idle_followup_cooldown_ms` (default 5 minutes) has elapsed since the last idle follow-up.\n4. Embedding coverage has progressed since the last check (stagnation guard).\n\nIf all are met:\n```\n:idle_maintenance_tick\n  └── maybe_schedule_idle_followup_reindex/1\n        └── {:prepare_reindex, idle_followup_mode}  ← idle catchup\n```\n\nBy default (`idle_followup_mode: :deep_dive_1`), this runs an embedding pass on already-discovered files without re-triggering a wasteful `quick_pass` structural scan. This is the primary mechanism keeping embeddings topped up in the background on a long-running server — you do not need to trigger it manually.\n\n### 4. Explicit reindex call (`synapse_index` MCP tool / `Indexer.reindex/2`)\n\nAn agent or operator calls `synapse_index(repo_id: \"...\", mode: \"full\")`:\n\n```\nIndexer.reindex(repo_id, mode)\n  └── handle_cast({:reindex, mode})\n        ├── if tasks in flight  → queued_reindex_mode (fires when pool drains)\n        └── if idle             → {:prepare_reindex, mode}\n```\n\n### 5. File watcher event (real-time update)\n\nWhen a file is saved, the `FileSystem` watcher emits `{:file_event, watcher, {path, events}}`. The Indexer debounces these events:\n\n```\n:file_event\n  └── buffer_file_event/2  (100 ms debounce window)\n        └── :flush_file_events\n              └── enqueue_manual_work(path, force: true, embed?: true)\n                    └── :run_phase_step  (high-priority manual queue)\n```\n\nA file-watcher trigger **does not** kick off a new full quick_pass — it only re-indexes the individual changed file through the manual queue. The manual queue always drains before normal phase work resumes.\n\n### 6. `synapse_index` with `path` (targeted reindex)\n\n`Indexer.index_path(repo_id, path)` casts `{:index_path, path, force}` directly into the manual queue — same hot path as file events, same no-full-scan guarantee.\n\n---\n\n### Summary table\n\n| Trigger | Full traversal? | Embeds? | Config key |\n|---|---|---|---|\n| Boot (`full` mode) | ✅ | ✅ | `boot_index_mode: :full` |\n| Boot (`quick_pass` mode) | ✅ | ❌ | `boot_index_mode: :quick_pass` |\n| Boot follow-up | ✅ | ✅ | `boot_followup_mode: :full` |\n| Idle follow-up | ❌ | ✅ | `idle_followup_mode: :deep_dive_1` |\n| `synapse_index` (full) | ✅ | ✅ | — |\n| `synapse_index` (quick_pass) | ✅ | ❌ | — |\n| File watcher event | ❌ | ✅ | — (per-file only) |\n| `synapse_index` with `path` | ❌ | ✅ | — (per-file only) |\n\n> **Why do I see repeated quick_passes?**\n> In dev, `boot_index_mode: :quick_pass` + `boot_followup_mode: :full` means every server restart fires:\n> 1. A quick_pass (structure only)\n> 2. A full deep-dive follow-up (which internally re-scans all files for embeddings)\n>\n> This is by design — it gives you queryable structure in seconds while embeddings catch up. If you want a single-shot full pass on boo","readmeFilename":"README.md"}