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configure BrainMCP guidance and MCP connections across agent projects","maintainers":[{"name":"brainmcp","email":"team@brainmcp.ai"}],"readme":"# `@brainmcp/brainmcp`\n\nSafely configure [brain / brainmcp](https://www.brainmcp.ai) guidance and MCP connections for agent clients.\n\nRequires Node.js 22 or newer. The recommended command runs the latest published CLI directly, so\nthere is no permanent global package to maintain.\n\nFull client walkthroughs: [Quickstart](https://www.brainmcp.ai/docs/quickstart) · [Claude Code](https://www.brainmcp.ai/docs/connect-claude-code) · [Cursor](https://www.brainmcp.ai/docs/connect-cursor) · [Codex](https://www.brainmcp.ai/docs/connect-codex) · [VS Code](https://www.brainmcp.ai/docs/connect-vscode) · [GitHub Copilot CLI](https://www.brainmcp.ai/docs/connect-copilot) · [Antigravity](https://www.brainmcp.ai/docs/connect-antigravity)\n\n## Quickstart — all projects, supported agents\n\nPreview one combined user-scope change for Claude Code, Cursor, Codex, VS Code, GitHub Copilot CLI, and Antigravity, then confirm once:\n\n```bash\nnpx --yes @brainmcp/brainmcp@latest init --all --scope user\n```\n\nThe `--yes` before the package name belongs to `npx`: it suppresses npm's package-download prompt.\nIt does **not** skip BrainMCP's file preview or confirmation. To automate both prompts only after\nreviewing the targets, add a second `--yes` at the very end.\n\nOnly pin a workspace at user scope when that same workspace should be the default in **every**\nproject. Otherwise omit it and use the OAuth authorization default or a project-scope override:\n\n```bash\nnpx --yes @brainmcp/brainmcp@latest init --all --workspace <workspace-id> --scope user\n```\n\nAfter setup:\n\n1. Sign in to the [brain dashboard](https://dash.brainmcp.ai) and create one workspace for the\n   project if it does not exist yet. Start with **Review required**.\n2. Restart every configured client you plan to use. Installation only writes the MCP endpoint and\n   guidance; it does not log the client in.\n3. Log each client in to brain:\n   - **Codex:** run `codex mcp login brain` and finish the browser flow. Generated TOML pins Brain's\n     stable public `codex` OAuth client and canonical resource so re-login recovers the same logical\n     connection rather than registering another DCR identity.\n   - **Claude Code:** start a session, run `/mcp`, select **brain**, then choose **Authenticate**.\n   - **Cursor:** open **Settings → Tools & MCP**, select **brain**, then connect/authorize it.\n   - **VS Code (Copilot Chat):** start **brain** from **MCP: List Servers** or its `mcp.json` CodeLens, choose **Auth**, and complete browser sign-in.\n   - **GitHub Copilot CLI:** run `copilot`, open `/mcp`, and authenticate **brain**. If it shows `needs-auth`, run `/mcp auth brain`.\n   - **Antigravity:** in the IDE open **Settings → Customizations** and **Authenticate** brain (or **… → MCP Servers** to confirm it is listed). In `agy`, run `/mcp`, select **brain**, and finish OAuth. Paste an authorization code back into settings if prompted.\n4. On the brain consent screen, review the scopes, select every workspace that connection may\n   reach, and choose its default workspace.\n5. In the project, ask: `Use brain to give me an overview of this workspace.` Confirm the\n   [dashboard Connect view](https://dash.brainmcp.ai/connect) changes from *waiting for first call*\n   to **Agent seen ... ago**.\n6. If the overview says the workspace is empty, copy and paste this second command into the\n   connected agent:\n\n   ```text\n   Use brain to bootstrap this project now. Inspect the repository comprehensively and propose the\n   most detailed durable initial graph that fits one valid brain_change_propose. Use Cores as stable\n   concepts; parent a focused Neuron when a broader Core genuinely owns it, while allowing honest\n   standalone flat Neurons. Add described cross-Core links. Report the proposal ID/status, coverage,\n   remaining gaps, and whether it was auto-applied or awaits Review. Do not claim the workspace is\n   populated until it is applied.\n   ```\n\n   The dashboard's **Context map → Bootstrap with your agent** control provides the full canonical\n   version, including coverage, safety, modeling, and deduplication requirements. The CLI also prints\n   that full prompt after installation.\n7. Follow the returned status. If the proposal awaits **Review**, approve, edit, or reject it. The\n   workspace is not populated until the proposal is applied.\n8. Leave the generated guidance enabled. It tells agents to orient and retrieve context before\n   non-trivial work, follow workspace Rules/Skills/Workflows, and propose only genuinely new durable\n   project knowledge afterward.\n\nNo API keys or OAuth secrets are written to config files.\n\n## Guidance included in the current release\n\nVersion `0.1.24` bundles guidance `2026.09.30`: knowledge classes, workspace\ninference (pick an authorized workspace and continue instead of asking which one), Context Paths\n(save an explanation only when asked, and only when `brain_context_path_create` is advertised),\nproactive proposals during authorized work, explicit Rule/account-library write limits, and\ncustomer-agent processing responsibility. It also retains sector discovery/filtering,\nNeuron `brain_remember` / `brain_amend` selection, advanced `brain_change_propose` operations,\nand capability-aware fallback for older MCP servers. The CLI installs the compact managed instruction block; generated plugin/shared Skills and the\nMCP handshake carry the full authoring workflow. Every graph change still uses the audited\nproposal pipeline. Sectors classify Cores/Neurons across hierarchy; Unassigned means no effective\nprimary, including nodes with secondary memberships.\n\n`0.1.19` (published 2026-10-02) adds companion dead-grant handling (see Credential\nstorage and safety boundaries). `0.1.20` (published 2026-10-02) also makes\n`brainmcp login` exit after success. `0.1.21` (published 2026-10-02) gives SessionStart orientation a 2.5-second budget\ninstead of a fixed 800 ms per request inside 1 second, so a slow or cold API no longer drops it;\nrerun `init` so VS Code/Copilot hooks get the longer host timeout. `0.1.22` (published 2026-10-02) refreshes an expired\naccess token before the request instead of after a 401, and reuses the token endpoint found at\nlogin, so a session that starts with an expired token makes two requests instead of four.\n`0.1.23` (published 2026-10-02, npm `latest`) raises the SessionStart budget to 4 seconds (VS Code/Copilot host timeout 6 seconds) so\nthe first orientation after the API has been idle still loads; rerun `init` after upgrading.\nPublished versions cannot be reused.\n\n`0.1.24` (not yet published; npm `latest` is still `0.1.23`): failures use the documented [exit codes](#exit-codes)\ninstead of always `1`, and `brainmcp whoami` exits `3` when signed out or when the sign-in must be renewed\n(it exited `0` through `0.1.23`). `capture now` reports a refused sign-in (`3`) or permission (`4`)\ninstead of a network error. Only `whoami` changes between zero and non-zero; a script that ran it\nwhile signed out and expected `0` must read the exit code or the JSON `status`.\n\nPublication and server deployment are separate: `@latest` downloads the published npm version,\nnot unpublished repository source. After the release is published, rerun the setup command below\nand restart/reconnect your clients to load refreshed guidance. Keep capture opt-in: upgrading\ninstructions does not authorize digest capture or grant companion OAuth consent.\n\n## Rerun to upgrade or repair\n\nRun the same `init` command again after upgrading the package or whenever Brain configuration or\ninstructions may have been damaged. Every run previews the repair before writing:\n\n- The reserved `brain` MCP server entry is rewritten to the selected client’s exact defaults for\n  the installed release, even if an older client shape or valid-but-corrupted value is present.\n- The Codex `[mcp_servers.brain]` table is restored even if its generated markers were removed.\n- BrainMCP-managed instruction regions are replaced with current guidance. Existing workspace\n  bindings survive unless `--workspace` supplies a replacement. Dedicated Cursor, VS Code, and\n  Antigravity project-rule headers are refreshed; files without managed blocks restore defaults.\n- Unrelated MCP servers, TOML tables, and text outside valid managed instruction blocks are kept.\n  Changed existing files receive backups, and the write is atomic.\n\nSyntactically invalid JSON/JSONC, a non-object server map, unmatched/duplicated markers, or\nanother ambiguous structure still fails closed instead of guessing across unrelated user content.\nUse a server name other than `brain` for a separately maintained custom connection.\n\n`doctor` compares the complete managed instruction block with the guidance bundled in the CLI\nbeing run. A current version marker alone is insufficient: altered content and missing/duplicate\nend markers are reported too. Without `--workspace`, an existing explicit workspace binding is\npreserved for comparison. Diagnosis is read-only; valid stale content can be repaired by rerunning\n`init`, while ambiguous shared markers must be resolved before the installer can safely proceed.\nThis does not query npm for a newer release or prove authenticated MCP access. Setup prints a\nread-only agent verification prompt for that final check.\n\nThe guidance teaches agents to reuse fresh context, recover omitted Rules, stop retrieving once\nthe task is grounded, amend existing concepts, and distinguish applied proposals from pending review.\n\nAnswer grounding is part of every installed managed block and the MCP workflow. Agents must connect\nmaterial claims to sources they actually read, separate direct source statements from inferences,\nassumptions, and unknowns, and state when Brain does not supply the answer. A related search hit is\nnot evidence for an outcome. Quotations, delivery receipts, saved explanations, and applied proposals\ndo not independently verify factual truth or an earlier agent's motivation. Context Paths must not\npad steps or sources, invent requirements, or turn expected benefits into measured results.\n\nCompanion orientation is a bounded packet. It identifies workspace ids and active refs,\nlabels Rule excerpts and omitted context, and reports failed or mismatched workspace responses.\nGrounding and recovery instructions survive the shared 2,400-character cap; up to eight workspace\npackets share the remaining budget, with additional omissions disclosed. Agents still read overview\nfor full binding context. Read-only or unknown companion grants do not receive write-back instructions;\nhost MCP permissions are checked independently.\nThese instructions are intended to reduce unsupported claims. Delivery regressions verify their\npresence; actual model behavior requires separate evaluation.\n\nCheck one client's exact schema and placement, managed guidance, canonical and compatibility OAuth\nmetadata, PKCE/DCR/refresh capabilities, and strict scoped 401 challenge. For Cursor, VS Code,\nGitHub Copilot CLI, and Antigravity, doctor also fails when the reserved `brain` entry exists in\nboth project and user MCP config scopes:\n\n```bash\nnpx --yes @brainmcp/brainmcp@latest doctor --client cursor --scope user\n```\n\n`--all` intentionally excludes `generic`: an unknown client has no universal global config path.\nKeep each named host's `brain` MCP server in either project or user scope, not both. Prefer a\nmaintained plugin when Claude Code or Cursor offers one; use the CLI when you want reviewable\nfilesystem configuration or no plugin is available.\n\n## Project-local alternative\n\nFor a single repository only, omit `--scope user` (or pass `--scope project`) and run from that repo root:\n\n```bash\nnpx --yes @brainmcp/brainmcp@latest init --client claude-code\n```\n\n## Optional persistent CLI\n\nIf you prefer a `brainmcp` binary on your `PATH` for repeated administration, install it globally:\n\n```bash\nnpm install --global @brainmcp/brainmcp@latest\nbrainmcp init --all --scope user\n```\n\nThe setup result is the same. The `npx` path avoids global package permissions and version drift;\nthe global path makes later `doctor`, `print`, and `remove` commands shorter.\n\n## Commands\n\n| Command | What it does |\n| --- | --- |\n| `init` | Preview and restore current MCP config + instruction defaults for a client; installs lifecycle hooks by default |\n| `init --all` | Preview one combined change for Claude Code, Cursor, Codex, VS Code, GitHub Copilot CLI, and Antigravity after duplicate-scope preflight |\n| `doctor` | Check host schema, placement, duplicate scopes, managed markers, full OAuth discovery, and strict auth challenge |\n| `print` | Print the canonical config and guidance without writing |\n| `remove` | Preview and remove BrainMCP-managed blocks and hooks |\n| `login` | Interactive companion OAuth sign-in with browser consent; OS vault first, file fallback only with `--allow-file-credentials` |\n| `logout` | Revoke the companion grant when possible and clear local credentials |\n| `whoami` | Show the current companion identity without echoing tokens |\n| `capture` | Manage affirmative session digest capture (`enable`, `disable`, `status`, `now`, `purge-local`) |\n\nEvery mutation shows a diff and asks for confirmation unless you append a trailing CLI `--yes`.\n\n```text\nbrainmcp init [--client <client>] [--workspace <id>] [--scope project|user] [--no-hooks] [--write-back-nudge] [--yes]\nbrainmcp init --all [--workspace <id>] [--scope project|user] [--no-hooks] [--write-back-nudge] [--yes]\nbrainmcp doctor [--client <client>] [--workspace <id>] [--scope project|user]\nbrainmcp print [--client <client>] [--workspace <id>] [--scope project|user]\nbrainmcp remove [--client <client>] [--scope project|user] [--yes]\nbrainmcp login [--capture-digests] [--allow-file-credentials] [--service-token-stdin] [--store-service-token] [--force] [--json]\nbrainmcp logout\nbrainmcp whoami [--json]\nbrainmcp capture [enable|disable|status|now|purge-local] [--dry-run] [--workspace <uuid>] [--include-prompts] [--yes] [--json]\n```\n\n### Exit codes\n\n| Code | Meaning | Typical causes |\n| --- | --- | --- |\n| `0` | Success | Command completed; `whoami` has a usable sign-in; `capture now` was delivered |\n| `1` | General error | Unclassified failure, a declined preview, or a manual capture the server rejected for good |\n| `2` | Usage error | Unknown command or option, conflicting or misplaced flags |\n| `3` | Authentication required | `whoami` is signed out or its sign-in expired or was revoked (JSON `status` `unauthenticated` / `reauth_required`); HTTP 401; capture needs `brainmcp login --capture-digests` |\n| `4` | Permission denied | HTTP 403, missing `digests:write`, a workspace outside the grant, or capture disabled by consent, project policy, or the server |\n| `5` | Configuration error | `doctor` found issues; a host config file cannot be parsed; conflicting managed markers or a manual `brain` entry; Brain already configured in the other scope; missing hook runtime; no capture ledger or workspace |\n| `6` | Network error | Connection failure or request timeout; `capture now` left the digest queued after a transport, 429, or 5xx failure |\n\n`brainmcp hook` always exits `0` and prints `{}` when it cannot help, so a hook never fails the host agent.\n\n### Clients\n\n| `--client` | User-scope paths (`--scope user`) | Project-scope paths (default) |\n| --- | --- | --- |\n| `claude-code` | `~/.claude.json`, `~/.claude/CLAUDE.md` | `.mcp.json`, `CLAUDE.md` |\n| `cursor` | `~/.cursor/mcp.json`, `~/.cursor/rules/brainmcp-workspace.mdc` | `.cursor/mcp.json`, `.cursor/rules/brainmcp-workspace.mdc` |\n| `codex` | `$CODEX_HOME/config.toml`, `$CODEX_HOME/AGENTS.md` (default `~/.codex`) | `.codex/config.toml`, `AGENTS.md` |\n| `vscode` | Default VS Code profile `mcp.json`; `~/.copilot/instructions/brainmcp.instructions.md` | `.vscode/mcp.json`, `AGENTS.md` |\n| `copilot` | `~/.copilot/mcp-config.json`; shared `~/.copilot/instructions/brainmcp.instructions.md` | portable `.mcp.json`, `.github/copilot-instructions.md` |\n| `antigravity` | `~/.gemini/config/mcp_config.json`, `~/.gemini/GEMINI.md` | `.agents/mcp_config.json`, `.agents/rules/brainmcp.md` |\n| `generic` | Conventional `~/.mcp.json`, `~/AGENTS.md` (only when your host recognizes them) | `.mcp.json`, `AGENTS.md` |\n\nIf you omit `--client`, the CLI detects a single obvious client from the project. Multiple matches require an explicit `--client`. Copilot is detected from `.github/copilot-instructions.md`; its portable project `.mcp.json` is also a Claude Code location, so choose `--client copilot` explicitly when needed. Antigravity is detected from `.agents/mcp_config.json` or `.agents/rules`, not from a shared `.agents/skills` directory. VS Code user scope targets the platform’s default local profile; named profiles, Insiders, remote SSH, WSL, and dev containers need their own setup in that environment.\n\nShared artifacts are reference-safe on removal: the user-level VS Code/Copilot instruction remains\nuntil neither config uses Brain, and the portable project `.mcp.json` entry remains while either the\nmanaged Claude Code or Copilot CLI setup still uses it.\n\n### Scope\n\n- `user` — write to the selected host’s supported per-user locations so brain is available across that host’s projects\n- `project` (default) — write only under the current repository\n\nCursor, Codex, VS Code, GitHub Copilot CLI, and Antigravity must keep `brain` in exactly one of these\nscopes. `init` refuses to create a competing entry and tells you which `remove` command resolves it;\n`doctor` reports both paths when an older setup already contains a duplicate.\n\n### Workspace\n\n`--workspace <id>` embeds the workspace id in the managed guidance block so agents orient to that workspace. Prefer this at project scope. At user scope it affects every project for that host, so use it only for a genuinely global default. Without it, `brain_workspace_overview` may use the authorization’s default workspace; agents call `brain_workspaces_list`, infer the best authorized match from the task and repository, state the assumption, verify it with overview, and continue even when several candidates fit. Workspace descriptions help matching; they do not override instructions.\n\n## Examples\n\n```bash\n# Cursor for all projects\nnpx --yes @brainmcp/brainmcp@latest init --client cursor --scope user\n\n# Antigravity for all projects\nnpx --yes @brainmcp/brainmcp@latest init --client antigravity --scope user\n\n# Standalone GitHub Copilot CLI for all projects\nnpx --yes @brainmcp/brainmcp@latest init --client copilot --scope user\n\n# Codex user-scope with workspace pin\nnpx --yes @brainmcp/brainmcp@latest init --client codex --workspace ws_abc --scope user\n\n# Single-repo only\nnpx --yes @brainmcp/brainmcp@latest init --client vscode\n\n# Preview / remove\nnpx --yes @brainmcp/brainmcp@latest print --client vscode --scope user\nnpx --yes @brainmcp/brainmcp@latest remove --client cursor --scope user\n\n# Companion CLI login (two-phase OAuth companion access)\nbrainmcp login\n\n# Inspect companion credentials and access\nbrainmcp whoami --json\n\n# Session digest capture (affirmative opt-in)\nbrainmcp capture enable --workspace 11111111-1111-4111-8111-111111111111\nbrainmcp capture now\nbrainmcp capture now --dry-run\nbrainmcp capture status --json\nbrainmcp capture disable\nbrainmcp capture purge-local\n```\n\n## Companion OAuth and Lifecycle Hooks\n\nBrainMCP supports a two-phase connection workflow:\n1. **Authorize the host agent** (Claude Code, Cursor, Codex, etc.) over MCP OAuth to enable tool calls.\n   In Cursor, use **Settings → Tools & MCP**, select **brain**, and connect. A successful\n   `brainmcp login` does not attach `brain_*` tools to the IDE agent.\n2. **Authorize the companion CLI** via `brainmcp login`. Reuses your existing browser session with prefilled Continue when eligible. Companion grants are non-billable, independent of the host grant, and held under the scope ceiling `graph:read skills:read workflows:read offline_access` (never `changes:write`).\n\nCompanion REST calls go to `https://api.brainmcp.ai` (`BRAINMCP_API_URL`). OAuth discovery uses\n`https://mcp.brainmcp.ai` (`BRAINMCP_OAUTH_ISSUER`). Do not point `BRAINMCP_API_URL` at the MCP\nhost: `/api/mcp/workspaces` is not served there. Self-hosted layouts that split those roles should\nset both variables independently.\n\n### Credential storage and safety boundaries\n\n- Credentials prefer the OS vault, with one item per Brain account. If it is unavailable, `brainmcp login --allow-file-credentials` stores tokens in owner-only files under `~/.brainmcp/accounts/<accountId>/` (directory `0700`, file `0600`, no symlinks, atomic write). Capture consent, queues, and session ledgers are namespaced the same way so switching accounts cannot reuse the previous identity's local state.\n- Vault reads require a marker in the selected Brain home; a fresh `BRAINMCP_HOME` does not adopt a machine-wide credential. Existing file credentials remain readable if a vault later becomes available. Legacy flat state migrates only when its previous account owner is known; unowned state is retained without assigning it to a replacement login.\n- Service token fallback uses `BRAINMCP_SERVICE_TOKEN` or `brainmcp login --service-token-stdin` (process-only unless `--store-service-token`). It cannot call `/orient` or enable automatic capture. Do not pass the token as a command-line argument.\n- Default orientation hooks fail open, send no prompt text, and do not treat prompts as `/orient` queries. Hooks use a project binding, authorization default, or sole authorized workspace; when unresolved, they hand selection to the host agent's inference workflow. Companion login is independent of host MCP access. `--no-hooks` skips hook install; `--write-back-nudge` is off by default.\n- `capture now` and its dry run select the latest ledger for the current project. Delivery also requires the same workspace and capture-consent revision. Older ledgers without a project binding need fresh hook activity before manual capture. A nudge-only ledger stores counters, never prompts, summaries, edited paths, or model labels.\n- Capture retries reserve a delivery lease and reuse the same digest ID. Concurrent hooks cannot enqueue the same session slice twice or send a manual item in the background. Consent and authorization are checked again immediately before sending, including after token refresh.\n- API and OAuth requests enforce deadlines through refresh and response-body reads, reject redirects, and keep remote error bodies out of diagnostics. Stored OAuth takes precedence over the service-token environment fallback; replacing a login verifies the newly issued token explicitly.\n- Once a refresh request is sent, the companion waits for the response and stores the rotated tokens even after the calling hook's deadline, so a refresh token the server already rotated is never discarded. When the token endpoint rejects the grant (`invalid_grant`, `invalid_client`, or `unauthorized_client`), the companion marks it for re-login: hooks stop sending requests, SessionStart tells the agent to orient through the host `brain_*` tools and to ask the user to run `brainmcp login` (no `--force` needed for a rejected grant), and `whoami` and `doctor` report it. Other orientation failures name their cause (`timeout`, `forbidden`, `http_<status>`, `network`) in the packet and in `orient_fetch_failed` diagnostics. A lapsed hourly access token with a refresh token is healthy.\n- Cloud environments (e.g. Cursor Cloud Agents, GitHub Codespaces without a local browser) do not share this machine's `~/.brainmcp` state; configure service tokens or dashboard connections for those environments.\n\n## What gets written\n\n- Canonical MCP endpoint: `https://mcp.brainmcp.ai/mcp` (server name `brain`)\n- Managed instruction markers (`brainmcp:managed:start` / `end`) so later `init` / `remove` can update safely\n- Task-first guidance: disclose connection/auth failures honestly, orient, start with a bounded search working set, escalate to exact or broader reads only when needed, and apply recent review feedback\n- Empty-workspace guidance: never silently omit bootstrap; after explicit authorization, study the project comprehensively and propose detailed concept Cores, focused Neurons with honest conceptual parenting (or legitimate flat placement), and described links; report whether the proposal was auto-applied or awaits Review\n- Selective write-back guidance: propose only new durable project knowledge, never store secrets/raw transcripts/temporary output, correct exact duplicate creates instead of retrying, report proposal status, and abstain when nothing reusable changed\n- Context Path guidance: save only on request and when advertised; cite nodes, Rules, Skills, direct instructions, and labeled assumptions; distinguish delivery evidence from reported influence; retry unchanged payloads with the same key and use a new key only for repaired payloads after definitive rejection\n- Backups for changed files; existing modes and symlinked dotfiles are preserved, and stale previews are refused\n- No embedded OAuth secrets — tokens come from the browser consent flow\n\n## Local package verification\n\nFrom this repository, run `corepack pnpm --filter @brainmcp/brainmcp test:package`. It packs\nthrough the `prepack` build, then checks the extracted package in disposable project and home\ndirectories for all six hosts, including installed guidance, the bundled Skill renderer, hooks, repeat initialization, and removal.\nIt does not install into your home or publish to npm. `npm pack` and source-directory publication\nboth rebuild the bundled guidance through `prepack`; do not use `--ignore-scripts` to prepare a release.\n\n## Requirements\n\n- Node.js 22+\n- A [brain](https://dash.brainmcp.ai) account and workspace for OAuth\n- A client version that supports remote HTTP MCP and browser OAuth\n\n## License\n\nMIT\n","readmeFilename":"README.md"}