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Run with any native coding agent.**","maintainers":[{"name":"bjornjac","email":"bjornjac@pm.me"}],"readme":"# agent-run\n\n**Config once. Run with any native coding agent.**\n\nFor persistent knowledge, shared skills, and tasks, use the bundled\n[`agent-brain` MCP server](#persistent-context-with-agent-brain). It runs as a per-user service\nhosted by `@technomoron/apicore-server` on a private Unix socket. Native agents\nconnect through a stdio-to-socket bridge.\nNode 24 or newer is required.\n\n`agent-run` lets you manage Codex, Claude Code, Gemini CLI, and Grok Build from\none shared configuration system while continuing to use each vendor's native\nagent.\n\nKeep agent configuration in a separate Git repository instead of adding\nagent-specific files to every codebase. Define project instructions, skills,\nMCP servers, policies, and reusable configuration fragments once, then generate\nthe native configuration each agent expects.\n\nConfiguration is template-based using Nunjucks/Jinja-style templates, making it\neasy to build hierarchical setups from global defaults, organization rules,\nproject-specific settings, reusable fragments, and local overrides.\n\n`agent-run` generates isolated agent runtimes outside the source repository, so\napplication repositories remain clean and developers do not have to maintain\nseparate `AGENTS.md`, `CLAUDE.md`, `GEMINI.md`, skills, and tool configuration\nfor every agent.\n\nThe core idea is simple:\n\n**One configuration repository. One set of skills. Multiple native agents.**\n\n```text\nshared config repository\n        ↓\nglobal + project + local templates\n        ↓\ncanonical instructions / skills / MCP\n        ↓\nagent-specific generated runtime\n        ↓\nCodex | Claude Code | Gemini CLI | Grok Build\n```\n\nThe native agents remain native. `agent-run` does not replace their execution\nengines, authentication, models, or tooling. It provides the portable\nconfiguration layer around them.\n\n**Config once, run anywhere.**\n\n## Model\n\nThere are three things:\n\n- the source tree\n- the agent config tree\n- this `agent-run` wrapper\n\nExample:\n\n```text\n~/.agent-run/\n  agent-run.defaults.jsonc\n  runtime/codex/         # shared, ignored Codex home\n    agent-run-<id>.config.toml\n    skills/agent-run-<id>/\n    sessions/\n    memories/\n  org/\n    my-api/\n      agent-run.jsonc\n      local.md.njk       # optional\n      overrides/         # optional\n      notes/\n        memory/\n          README.md      # durable project memory, normally tracked\n      live/\n        CLAUDE.md\n        .claude/         # Claude settings, MCP, and skills\n        bin/\n        memories/\n          codex-home/\n            AGENTS.md\n            config.toml\n        gemini/\n          AGENTS.md\n          settings.json\n          home/          # private Gemini state and generated skills\n        grok/\n          AGENTS.md\n          config.toml\n          skills/\n~/source/org/my-api/\n```\n\nIf your source repo is `~/source/org/my-api`, `agent-run` maps it to:\n\n```text\n~/.agent-run/org/my-api\n```\n\nThe source repo stays clean. The agent files live in the matching path under\nthe agent config tree.\n\n## File Roles\n\n- `agent-run.defaults.jsonc`: config-root defaults shared by every profile\n- `agent-run.jsonc`: sparse profile manifest and profile-discovery marker\n- `local.md.njk`: optional project-specific instructions\n- `overrides/`: optional per-profile template overrides\n- `notes/memory/`: durable project memory shared through the config repository\n- `live/memories/codex-home/AGENTS.md`: generated Codex instructions\n- `live/memories/codex-home/config.toml`: rendered Codex template for inspection\n- `<config-root>/runtime/codex/`: shared Codex home, authentication and session state\n- `runtime/codex/agent-run-<id>.config.toml`: named Codex profile with project instructions and settings\n- `runtime/codex/skills/agent-run-<id>/`: generated skills, enabled only for that profile\n- `live/CLAUDE.md`: generated Claude instructions\n- `live/.claude/`: generated Claude settings, MCP configuration, and local\n  plugin skills\n- `live/gemini/`: generated Gemini instructions, settings, skills, and private\n  runtime state\n- `live/grok/`: generated Grok instructions, configuration, skills, and private\n  runtime state\n\nEdit only the root defaults and profile overrides that differ. `agent-run` keeps\ngenerated files in sync.\n\n## Native Agent Adapters\n\nEach supported CLI is isolated behind an adapter in `src/agents/`. The shared\nflow is:\n\n```text\nprofile and templates\n        ↓\ncanonical instructions, skills, and MCP servers\n        ↓\nCodex | Claude | Gemini | Grok adapter\n        ↓\nprivate generated runtime\n        ↓\nnative vendor CLI in the real project directory\n```\n\nCodex, Gemini, and Grok receive the same generated `AGENTS.md` content. Claude\nreceives a thin `CLAUDE.md` serialization of those same canonical instruction\nsections. Vendor-specific paths, settings formats, environment variables, and\nlaunch flags stay inside the matching adapter.\n\n## Manifest Defaults\n\nManifest values are resolved in this order:\n\n1. built-in defaults\n2. `<config-root>/agent-run.defaults.jsonc`\n3. `<config-root>/<profile>/agent-run.jsonc`\n\nNested manifest objects are merged. Arrays such as `checks`, `agent.includes`,\nand `skills.install` replace the inherited array instead of being appended.\nThe profile name is always inferred from project mapping; the root defaults file\nmust not set `profile`.\n\nA profile with no differences from the root defaults needs only this marker:\n\n```json\n{}\n```\n\nEnable or disable native agents under `tools`:\n\n```json\n{\n  \"tools\": {\n    \"codex\": true,\n    \"claude\": true,\n    \"gemini\": true,\n    \"grok\": true\n  }\n}\n```\n\nMCP servers have one canonical manifest representation. A server uses either a\nlocal command or a remote URL:\n\n```json\n{\n  \"mcp\": {\n    \"servers\": {\n      \"local-tools\": {\n        \"command\": \"node\",\n        \"args\": [\"/opt/team-mcp/server.js\"],\n        \"env\": {\n          \"TEAM\": \"docs\"\n        }\n      },\n      \"remote-tools\": {\n        \"transport\": \"http\",\n        \"url\": \"https://mcp.example.com/mcp\",\n        \"enabled\": true\n      }\n    }\n  }\n}\n```\n\n`transport` may be `stdio`, `http`, or `sse`; it is inferred as `stdio` when\n`command` is present and `http` otherwise. The adapters serialize enabled\nservers into each CLI's native MCP format. Disabled servers remain disabled in\nCodex and Grok and are omitted from Claude and Gemini.\n\n`local.md.njk` and `overrides/` are not created unless they contain actual\nprofile-specific configuration.\n\n## Guard Shims\n\n`blockGitWrite`, `blockPublish`, and `blockGithubRelease` put small `git`, `npm`,\n`pnpm`, and `gh` shims on the launched agent's `PATH`. They refuse\n`git commit`, `git tag`, `git push`, `npm publish`, `pnpm publish`, and\n`gh release create` with exit code 42 and pass everything else through to the\nreal command. Set `AGENT_RUN_ALLOW_GIT_WRITE=1`, `AGENT_RUN_ALLOW_PUBLISH=1`, or\n`AGENT_RUN_ALLOW_GITHUB_RELEASE=1` for a single invocation you have reviewed.\n\nThrowaway repositories that a test suite creates and deletes are exempt from the\n`git` shim. Create an empty `.agent-run-test-repo` file in the repository, or in\nany directory above it, and `git commit`, `git tag`, and `git push` run normally\nfor anything below that marker. The shim reads the marker from the directory\n`git` would work in, following any leading `-C` options. This is what lets\n`pnpm test` run inside an agent session; nothing outside a marked directory is\naffected.\n\n## Profile Resolution\n\nThe mapped path is:\n\n```text\n<config-root>/<profile>\n```\n\n`profile` is resolved in this order:\n\n1. `AGENT_RUN_PROFILE` in `.agent-run.env`\n2. Registered agent-brain source root (the most specific match)\n3. GitHub `origin` remote\n4. `package.json.repository` (string or object `url`)\n5. `package.json.name`\n6. The project path as `[parent]/[current]`\n\nExamples:\n\n- `AGENT_RUN_PROFILE=org/my-api` -> `org/my-api`\n- `AGENT_RUN_PROFILE=unrelated/hello` -> `unrelated/hello`\n- `package.json.repository = \"github:org/my-api\"` -> `org/my-api`\n- `package.json.name = \"@org/my-api\"` -> `org/my-api`\n- `package.json.name = \"my-api\"` -> `my-api`\n- `/work/org/my-api` with none of the above -> `org/my-api`\n\n`AGENT_RUN_PROFILE` is relative to the config root. It is not a filesystem\npath, so values like `/tmp/foo`, `C:/tmp/foo`, or `../foo` are rejected.\n\nThe path fallback lets plain directories work without a Git repository or a\n`package.json`. The explicit profile sources above always take precedence.\nWith agent-brain enabled, an unconfigured directory uses the default profile.\nAn explicit `AGENT_RUN_PROFILE` still takes precedence, and namespaced brain\nproject names resolve to their registered profiles.\n\n## Overrides\n\nLocal override for a repo:\n\n```dotenv\n# .agent-run.env\nAGENT_RUN_PROFILE=org/my-api\n```\n\nConfig root:\n\n- default: `~/.agent-run`\n- override with `--configdir=/path/to/agent-configs`\n- override with `AGENT_CONFIG_DIR=/path/to/agent-configs`\n- or set `AGENT_CONFIG_DIR=/path/to/agent-configs` in `.agent-run.env`\n\n## Commands\n\nGlobal flag:\n\n- `-h`, `--help`: show wrapper help for `agent-run` and the built-in commands\n- `-v`, `--verbose`: print path resolution, file creation, include expansion,\n  generated file writes, and spawned commands\n\n`agent-run codex --help`, `agent-run claude --help`, `agent-run gemini --help`,\nand `agent-run grok --help` pass `--help` through to the underlying tool.\n\nFor any native agent command, use `--generate` to generate profile files\nwithout launching the underlying tool.\n\nCodex defaults to `-a on-request -s workspace-write`. `agent-run` uses one\n`CODEX_HOME` at `<config-root>/runtime/codex` and selects a generated named\nprofile with `--profile`. Project instructions are added through\n`developer_instructions`; MCP settings and per-skill enablement stay in the\nnamed profile. The normal global Codex executable is used. Codex 0.157.0 runs\nnamed-profile sessions with its embedded backend, avoiding automatic daemon\npackage copies and the long per-project Unix socket path. Agent-run does not\nadd `--no-daemon`. This layout requires Codex with named profile-file support\n(0.134.0 or newer); Windows and Debian are tested with 0.157.0.\n\nCodex starts from the project root, also passed with `-C`, with generated guard\nshims on `PATH`. Use `--network` to enable network access in the workspace-write\nsandbox. Windows profiles default to the native unelevated sandbox unless the\nprofile template specifies another mode. When `~/.codex/auth.json` exists, the\nshared home links that login cache (copies it when Windows cannot create file\nsymlinks), so changing projects does not require another login.\n\nOn first use of each old project home, agent-run copies its `sessions/` and\n`archived_sessions/` rollouts into the shared home without overwriting existing\nfiles. Codex rebuilds its derived session index. Original files, databases,\nhistory, native memories and old daemon packages remain untouched in the old\nhome; databases and daemon installations are not copied. Close old agent-run\nsessions before upgrading so their final turns are included. New sessions and\nnative memories use the shared home; durable project knowledge remains separate.\n\n### Project Memory\n\nEach profile has a durable `notes/memory/` directory outside the source repo.\n`README.md` is a short index; agents read only the linked files relevant to the\ncurrent task. Agents may update project memory when the user explicitly requests it or\nauthorizes a standing workflow, such as saving durable corrections and updating\naffected specs. This authorization does not permit Git or external-service writes.\n\nCodex's native `$CODEX_HOME/memories/` lives in the ignored shared home. It\nis generated, machine-local recall data and is not copied into the tracked\nproject memory directory. Project memory is plain Markdown so it can be\nreviewed and shared through the Git repository that normally holds the\n`.agent-run` config tree.\n\nWith agent-brain enabled, `memory/` is the canonical project knowledge directory\nand remains in place; existing `notes/memory/` is also read. Without agent-brain,\nlegacy `memory/` moves to `notes/memory/`. Loose `memory*.md` files and Markdown\nfiles directly under the old `memories/` directory move to the applicable memory\ndirectory. Agent-run detects the old layout\nbefore updating or launching an agent. If those files are tracked, agent-run\nshows the moves and asks before staging them with `git mv`. In a non-Git config\ntree, or for untracked files, it uses ordinary filesystem moves. Non-interactive\nruns stop with a command that can confirm the migration explicitly.\n\nClaude Code currently has no `--cd` equivalent. `agent-run` keeps Claude's\nprocess cwd at the project root, appends the generated `CLAUDE.md` with\n`--append-system-prompt-file`, passes generated settings with `--settings`, and\nloads generated skills from a local plugin with `--plugin-dir`. It does not\nreplace the user's normal `CLAUDE_CONFIG_DIR`. If Claude writes remembered\npermissions to `.claude/settings.local.json`, `agent-run` removes that file\nafter the session unless `--local` was used.\n\nGemini runs from the real project directory with a private\n`GEMINI_CLI_HOME`. Its generated system settings configure `AGENTS.md` as the\ncontext filename and add the private runtime plus project memory as context\ndirectories. Generated skills use Gemini's `.agents/skills` alias. Existing\nGemini login credentials, commands, and user skills are linked into the private\nhome when present. On Windows, shared user preferences and generated settings\nare merged into the private home's `.gemini/settings.json`; shared settings\nremain untouched. This avoids Gemini's administrator-only system-settings ACL\nrequirement. On other platforms, user settings are linked and generated system\nsettings remain the highest-priority project layer. Gemini's normal folder-trust\nand sign-in requirements still apply.\n\nGrok runs from the real project directory with `GROK_HOME` set to\n`live/grok/`. Grok natively reads the generated home-level `AGENTS.md`,\n`config.toml`, and `skills/`. Existing Grok login and MCP OAuth credential\nfiles are linked into the private runtime when present.\n\n`--yolo` runs the selected tool unattended, with no approval prompts: Codex\nwith `-a never -s danger-full-access`, Claude with\n`--dangerously-skip-permissions`, Gemini with `--yolo`, and Grok with\n`--always-approve`.\nOnly use it when the agent may change or delete anything it can reach. Claude\nrefuses `--dangerously-skip-permissions` when it runs as root, so run it as a\nnormal user. `--sandboxed` selects the native workspace sandbox for Codex,\nGemini, or Grok. `--network` remains Codex-only.\n\nBy default, all four native agent commands fail when local AI files such as\n`AGENTS.md`, `CLAUDE.md`, `GEMINI.md`, `.mcp.json`, `.agents`, `.claude`,\n`.codex`, `.gemini`, or `.grok` are present inside the project repository. Use\n`--local` to warn and continue for a specific invocation.\n\nShow the native capability matrix:\n\n```sh\nagent-run status\n```\n\nInitialize mapped files for the current repo:\n\n```sh\nagent-run generate\n```\n\nThis creates `<config-root>/agent-run.defaults.jsonc` when needed and a minimal\n`agent-run.jsonc` marker for the mapped profile. It does not create empty local\ninstruction or override files. `agent-run init` remains as a deprecated alias.\n\nEdit the source file for the current repo:\n\n```sh\nagent-run edit\n```\n\nThis creates `local.md.njk` when needed, syncs generated files, then opens it in\nyour editor.\n\nRegenerate the generated files for the current repo:\n\n```sh\nagent-run update\n```\n\n`update` requires an existing profile marker or local/legacy instruction file;\nit does not silently scaffold an unconfigured project. Use `agent-run generate` or\nthe tool command's `--create` option first.\n\nRegenerate every profile under the config root without requiring matching code\ncheckouts:\n\n```sh\nagent-run update --all ~/.agent-run\n```\n\nIf the config root argument is omitted, `update --all` uses the normal configured\nroot. Without an override, the root is `$HOME/.agent-run`.\n\nYou can also generate from a tool command and stop before launch:\n\n```sh\nagent-run codex --generate\nagent-run claude --generate\nagent-run gemini --generate\nagent-run grok --generate\n```\n\nThis reads the root defaults, sparse profile manifest, and Nunjucks templates,\nthen rewrites generated files:\n\n- `live/CLAUDE.md`\n- `live/memories/codex-home/AGENTS.md`\n- `live/memories/codex-home/config.toml`\n- `<config-root>/runtime/codex/agent-run-<id>.config.toml`\n- `<config-root>/runtime/codex/skills/agent-run-<id>/**`\n- `live/.claude/**`\n- `live/gemini/**`\n- `live/grok/**`\n- `live/bin/**`\n\nPer-profile override templates can be placed in:\n\n- `overrides/codex-config.toml.njk`\n- `overrides/claude-settings.json.njk`\n- `overrides/gemini-settings.json.njk`\n- `overrides/grok-config.toml.njk`\n\n## Default Config Tree\n\nA complete default tree lives in `examples/basic-config`. It includes a minimal\nproject, `.agent-run.env`, root manifest defaults, global templates and\nsnippets, profile-local templates, skill templates, a personal memory skill,\nprofile skill overrides, tool config overrides, guardrails, checks, and\ngenerated runtime paths.\n\nTo install the default tree and detected profile in your resolved config root:\n\n```sh\nagent-run setup\n```\n\nOr select a profile non-interactively:\n\n```sh\nagent-run setup myorg/myrepo\n```\n\nUse `--configdir=DIR` to choose a different destination. The copy skips files\nthat already exist, so local edits are preserved.\n\nTry it from a checkout:\n\n```sh\npnpm build\nnode dist/agent-run.js update examples/basic-config/project\nnode dist/agent-run.js check examples/basic-config/project\n```\n\nTo add persistent knowledge and tasks to the starter, first copy its\n`agent-config/` directory outside your source repository, then run\n`agent-brain init --configdir /path/to/agent-config`. Existing profiles are\npreserved, and the brain MCP connection is added on the next generation or\nlaunch. [brain.example.jsonc](examples/basic-config/brain.example.jsonc) shows\nthe optional root configuration; the starter commands do not enable it.\nGenerated starter runtime files live below\n`examples/basic-config/agent-config/starter/basic-project/live/`.\n\nCheck the current repo:\n\n```sh\nagent-run check\n```\n\nThis reports:\n\n- local AI files accidentally present in the source repo\n- missing mapped files\n- stale generated instructions, settings, MCP configuration, or skills for any\n  enabled native agent\n- invalid generated JSON or skill metadata\n- profile resolution problems\n\nCheck every repo under a source tree:\n\n```sh\nagent-run check --all ~/source\n```\n\nMigrate an existing config tree to the manifest/template layout:\n\n```sh\nagent-run migrate-config --yes ~/.agent-run\n```\n\nThis preserves `AGENTS-MODS.md`, creates `local.md.njk` and a sparse\n`agent-run.jsonc` marker for legacy profiles, creates the root defaults and\n`global/` templates, moves loose review files into `reviews/`, moves loose\nproject memory files into each profile's `notes/memory/`, and moves old Codex\nruntime files into `live/memories/codex-home` without overwriting existing\nfiles. Use `--yes` to confirm tracked `git mv` operations in a non-interactive\nrun. Omit `--yes` to review and confirm tracked moves interactively. The\ncommand stages moves but never commits them.\n\n## Persistent context with agent-brain\n\n`agent-brain` gives the native agents the same project knowledge, skills, and\ntasks through MCP. It uses the official Node MCP SDK. The persistent\nservice runs under `@technomoron/apicore-server` on a private Unix socket or a\nWindows named pipe restricted to the current user, SYSTEM, and administrators.\nNode 24 or newer is required; SQLite and FTS come from Node, with no database\npackage to compile.\n\nOrdinary questions, explanations, and conversation do not need brain lookups\nunless the answer depends on saved project knowledge. Before substantial\nimplementation or project changes, agents retrieve relevant constraints and\napplicable skills, reusing context already loaded in the conversation. Skill\nlisting is only needed to discover a skill. Asking an agent to do work does not\nby itself authorize creating a saved todo; task tracking needs a user request or\nan explicitly authorized task-tracking workflow.\n\nAfter upgrading, run `agent-run update` to refresh generated instructions.\nExisting custom templates and installed skills are preserved. If they require\nbrain calls before every action or automatic task creation, narrow those rules\nin their source files; updating does not rewrite customized instructions.\n\n### Start using it\n\n```sh\nagent-brain init\nagent-brain serve\n```\n\nKeep the service running, or enable the systemd user service described below.\nIn another terminal:\n\n```sh\ncd ~/code/my-project\nagent-run create my-project --quick\nagent-run codex\n```\n\nOmit `--quick` for the short interactive setup, or use `--guided` to add an\narchitecture summary, constraints, conventions, and a preferred agent.\nCreation detects the source root, Git remote, languages, package manager,\ndocumentation, and package scripts. It writes configuration outside the source\nrepository. Existing directories and duplicate project registrations are rejected.\n\n`agent-run project list` lists registrations. `project info` shows the current\nproject, and `project bootstrap` returns detected information for the agent to\ninspect and turn into proposals. Bootstrap does not invent or save architectural\nfacts; the agent can use the knowledge tools after the user confirms its proposals.\n\nAll commands accept `--configdir PATH`. Brain commands also accept `--cwd PATH`.\n`agent-brain --help` lists the commands.\n\n### Scopes and existing profiles\n\n```text\n~/.agent-run/\n  brain.jsonc\n  global/skills/<name>/SKILL.md\n  global/constraints/*.md\n  projects/my-project/\n    agent-run.jsonc\n    config.yaml\n    project.md\n    memory/*.md\n    todo/*.md\n    live/\n  default/\n    agent-run.jsonc\n    skills/\n    preferences/\n    constraints/\n    conventions/\n    reviews/\n    memory/*.md\n    todo/\n    templates/\n    live/\n  index/knowledge.sqlite\n  runtime/\n```\n\nInside a registered or existing configured project, retrieval includes global\nand project knowledge. Elsewhere it includes global and default knowledge.\nDefault knowledge never appears in a configured project. Among registered\nsource roots, the most specific matching root wins; equal matches are rejected.\nAn explicit `AGENT_RUN_PROFILE` in `.agent-run.env` keeps precedence over registration.\n\nProject names can include a namespace: `technomoron/agent-run` lives under\n`projects/technomoron/agent-run`. The original name also works in\n`AGENT_RUN_PROFILE`; no alias is needed.\n\nExisting JSONC manifests, Nunjucks templates, and `org/repo` profiles remain\nsupported. Brain reads existing `notes/memory` directories in place, including\nthe config root's global notes. It does not move or delete them. New knowledge\nuses the directories above. Existing files without metadata are treated as\ninferred, relevant-only knowledge; adding metadata gives you explicit control.\nLegacy review metadata is preserved, and reviews marked addressed or resolved\nare excluded from active recall. Canonical `global/skills/<name>/SKILL.md` files\nalso support existing Nunjucks variables when served or rendered for native agents.\n\n`agent-brain init` installs the shared brain skills and a default profile, and\ncreates `brain.jsonc` only if it does not exist. It preserves existing files.\nIt creates the topic directories shown above in global, default, and registered\nproject scopes, plus `rules/`, `decisions/`, `specs/`, and `observations/` for\nthe other knowledge types. Project creation uses the same layout. Empty topic\ndirectories stay empty until there is relevant content to store.\nNormal profile rendering then adds the brain MCP server and shared instructions\nto Codex, Claude, Gemini, and Grok. An explicitly configured `agent-brain` MCP\nentry takes precedence. Set `enabled` to `false` to stop automatic integration\nand restore the previous unconfigured-project behavior.\n\n```jsonc\n{\n  \"enabled\": true,\n  \"contextBudget\": 16000,\n  \"connectors\": {}\n}\n```\n\n`contextBudget` counts serialized characters, not model tokens. A context result\nreports omitted items. Use `get_knowledge` to read complete items when necessary.\nAlways-recalled knowledge is considered first, then matching file patterns,\nthen lexical results. Search uses FTS ranking with extra weight for titles and tags.\nQueries compare the current files with the index and write only added, changed,\nor removed entries. Unchanged queries do not take a database write lock. Context\nretrieval scans the files once. Search and context MCP tools declare that they\nmay write because they can refresh this derived index.\nSymbols contribute search terms. Manual Markdown changes are read on every query;\nthe index can be deleted while the service is stopped and rebuilt on the next query.\n\n### Knowledge and skills\n\nMalformed knowledge and task files do not block other entries. When a scan finds\nproblems, MCP and CLI list/search responses contain `items` and `brokenFiles`;\nobject responses, including context, gain a `brokenFiles` field. Each error lists\nthe source path, `status: \"broken\"`, a reason, and an ID when it can be parsed.\nResponses without errors keep their existing format. Broken entries are excluded\nfrom search and context, and reads or updates of those entries are refused.\nCorrect the file on disk; the next scan picks up the repair automatically.\nDuplicate IDs flag all matching files. External task imports and new review\nnumbering stop when broken files would make deduplication or numbering unreliable.\n\nKnowledge is one Markdown file per item, with YAML metadata:\n\n```markdown\n---\nid: auth-refresh-single-use\ntype: constraint\nscope: project\nauthority: user\nstatus: active\nrecall: always\ntags: [auth]\napplies_to: [\"src/auth/**\"]\ncreated: 2026-09-06\n---\n\n# Refresh tokens are single-use\n\nA successfully consumed refresh token must never be accepted again.\n```\n\nThe storage directories are `rules`, `preferences`, `conventions`, `constraints`,\n`decisions`, `specs`, `reviews`, `memory`, and `observations`. Scope metadata must\nmatch the file's directory. IDs must be unique across the active scopes.\nInvalid metadata produces an error identifying the file. Symlinked storage\npaths are rejected. Individual Markdown files are limited to 1 MiB.\n\nChoose the scope and singular knowledge type when calling `remember`; MCP writes\nthe file into the corresponding directory. User preferences belong in\n`preferences/`, requirements in `constraints/`, established practices in\n`conventions/`, confirmed specifications in `specs/`, and confirmed choices in\n`decisions/`. Code-derived facts remain inferred `observations/`; source\nreferences and history belong in `memory/`, with planned features labeled as\nplans. An import request does not make inferred content authoritative.\nUse the todo tools for tasks. Reusable workflows are `skills/<name>/SKILL.md`\nfiles, and reusable templates belong in `templates/`; `remember` does not\ninstall either. Global skills remain available without copying them into each\nproject. The brain-memory skill explains these choices to native agents.\n\nAvailable MCP tools include `get_context`, `search_knowledge`, `get_knowledge`,\n`remember`, `amend_knowledge`, `list_knowledge`, `archive_knowledge`,\n`knowledge_history`, `promote`, `deprecate_knowledge`, `review_context`,\n`review_list`, `resolve_review`, `review_history`, and `review_archive`.\nWrites use atomic file replacement and a shared lock; concurrent writes either\ncomplete or report that the caller should retry. After a crashed writer, stop\nthe service, verify the PID in `runtime/brain-write.lock` is no longer running,\nand remove that lock before restarting.\n\n```sh\nagent-brain remember --json '{\"scope\":\"project\",\"type\":\"observation\",\"title\":\"Refresh handling\",\"content\":\"Investigate concurrent refresh requests.\"}'\nagent-brain search \"refresh\"\nagent-brain get ITEM_ID\nagent-brain amend ITEM_ID --revision REVISION --json '{\"content\":\"Corrected text.\"}'\nagent-brain deprecate ITEM_ID --revision REVISION \"No longer applies\"\nagent-brain promote ITEM_ID --scope global --revision REVISION --confirmed\n```\n\n`amend_knowledge` revises an active item in place, keeping its id, file name, scope,\ntype, authority, and history, and updating only the fields you pass. Use it to correct\nor extend knowledge instead of writing a near-duplicate. Scope, type, authority, and\nreview severity are not amendable; if one of those is wrong, deprecate the item and\nwrite a corrected one.\n\n#### Knowledge consolidation\n\nRun the consolidation skill from the current project's directory:\n\n```sh\nagent-run compress\nagent-run compress --dry-run\nagent-run compress --agent claude\nagent-run compress --scope global\n```\n\nThis opens the selected agent with the consolidation task and its normal generated\nconfiguration and permission settings. It uses project scope when configured,\notherwise default scope. Global knowledge changes require `--scope global`.\n`--dry-run` asks the agent to inspect and propose changes without modifying knowledge.\nAgent-brain must be initialized and its service available.\n\nChoose the user default in `<config-root>/agent-run.defaults.jsonc`:\n\n```jsonc\n{\n  \"agent\": {\n    \"default\": \"codex\"\n  }\n}\n```\n\nThe same field in a profile's `agent-run.jsonc` overrides the user default;\n`--agent` overrides both. Supported values are `codex`, `claude`, `gemini`, and\n`grok`. Older manifests without this field use Codex, and initialization preserves\nexisting configuration and customized skills. Explicit commands such as\n`agent-run claude` continue to select that agent directly.\n\nThe `brain-consolidate` skill removes repetition, combines focused topic records,\nand extracts appropriately classified knowledge from memory. It preserves\nrequirements, exceptions, authority, sources and useful history. Historical plans\nand inferred observations do not become confirmed requirements through compression.\nUnresolved contradictions remain visible. Reviews and tasks have separate workflows.\n\nClear, authoritative corrections in supplied comments or memory are reconciled\ninto the affected spec sections, preserving unrelated requirements and source\nreferences. A newer timestamp or code comment alone does not establish authority.\nSections explicitly marked immutable or locked are preserved verbatim unless the\nuser explicitly authorizes changing them. Conflicts with locked sections are\nreported while independent updates can proceed. These are skill instructions;\nthe storage API does not enforce section-level locks.\n\nThe command uses an installed skill override when present, otherwise the bundled\nskill; `agent-brain init` installs missing built-in skills without replacing existing ones.\n\n`list_knowledge` provides a complete paginated inventory of metadata and content\ncharacter counts, with `scope`, `types`, `includeDeprecated`, `offset`, and `limit`\n(default 50, maximum 100). It also reports `contextBudget`. Fetch complete records\nwith `get_knowledge` before editing; search and context results are not inventories.\n\nAfter writing and verifying replacements with `remember` or `amend_knowledge`,\n`archive_knowledge` accepts a request such as:\n\n```json\n{\n  \"sources\": [{\n    \"id\": \"old-id\",\n    \"revision\": \"<last-read SHA-256>\",\n    \"replacements\": [{\"id\": \"surviving-id\", \"revision\": \"<verified SHA-256>\"}]\n  }],\n  \"reason\": \"Combined duplicate requirements; verified all exceptions survive.\"\n}\n```\n\nEach source can point to multiple replacements when extracting different categories.\nThe tool checks all sources and replacements before writing, requires matching scope\nand authority, preserves recall coverage, and excludes reviews. The agent verifies\nsemantic coverage; the tool cannot prove that a summary preserves every fact.\nExact original files and replacement IDs/revisions go into one\n`knowledge-history.jsonl` per scope before source files are removed. If deletion\nfails, originals remain in history and an identical request can finish deletion\nwhile the supplied revisions still match. History and removed knowledge paths\nparticipate in authorized brain Git sync; compression itself never commits or pushes.\n\nUse `knowledge_history` with an old `id` to retrieve the original file text and\nreplacement references. Without `id`, it returns compact metadata; optional\n`scope`, `query`, `offset`, and `limit` support browsing. Follow replacement IDs\nthrough history if those records were later consolidated. Archived originals stay\nout of normal retrieval. This reduces active files and context text, while retaining\narchive bytes on disk.\n\nThe corresponding CLI commands accept the same JSON options:\n\n```sh\nagent-brain list --json '{\"scope\":\"project\",\"offset\":0,\"limit\":50}'\nagent-brain history --json '{\"id\":\"old-id\"}'\nagent-brain archive --json '<sources-and-replacements-object>'\n```\n\n#### File names\n\n`remember` names each file after the item id. Pass `filename` to choose the name\ninstead, as lower-case words separated by single dashes and no extension:\n\n```sh\nagent-brain remember --json '{\"scope\":\"project\",\"type\":\"observation\",\"title\":\"Build flow\",\"content\":\"...\",\"filename\":\"build-flow\"}'\n```\n\nIf that name is taken, the item id is appended rather than overwriting anything. The\nname is storage only and is never written into the metadata: the `id` in the front\nmatter is the identity, so files stay safe to rename by hand and the item is still found\nby id afterwards.\n\n#### Review findings\n\nReview knowledge is a numbered, prioritized list. `remember` requires a\n`severity` of `critical`, `high`, `medium`, or `low` when the type is `review`,\nand rejects `severity` for every other type. The store assigns the finding\nlabel itself: `C1`, `H1`, `M1`, `L1`, counting up per severity within the scope.\nResolved numbers are never handed out again, so a label always refers to the\nsame finding.\n\nEach finding also carries a `state` of `open`, `fixed`, or `wontfix`, separate\nfrom the `active` and `deprecated` status that controls recall. New findings\nstart `open`.\n\n```sh\nagent-brain review list\nagent-brain review list --severity high --state open\nagent-brain review resolve ITEM_ID --revision REVISION --state fixed \"Fixed by using a stable command name\"\n```\n\n`review_list` returns findings in severity then number order, open ones only\nunless states are given, each with the revision needed to resolve it.\n`resolve_review` records the state and reason and takes the finding out of active\nrecall. It writes a short record (label, title, outcome, date, reason, and original\nfile/revision) to the scope's `review-history.jsonl`, then deletes the full finding\nfile. `review-counters.json` preserves numbering. These files participate in brain\nGit sync but are excluded from normal knowledge retrieval.\n\nUse MCP `review_history` to recall old fixes, with optional `query`, `scope`, `state`,\n`offset`, and `limit` (default 100). The CLI equivalent is\n`agent-brain review history [query]`. Git retains full details only when the original\nfiles were committed before cleanup; the MCP history is sufficient for the short fix list.\nUse `review_archive` with a scope, or `agent-brain review archive --scope project`,\nto compact existing files already marked `fixed` or `wontfix`. Deferred findings\nremain open. Mark a finding `wontfix` only when the user explicitly drops it or\nconfirms it is intentional. A request to postpone an issue does not close it.\n\nFinding labels are indexed, so `search_knowledge` for `H2` finds that finding.\nReview files written before these fields existed keep parsing; they simply carry\nno label and stay out of the finding list.\n\nRemembered deductions default to inferred authority and must remain observations,\nmemories, or review records. Global writes require explicit user authority.\nPromotion copies an item, records its origin, preserves the original, and requires\nconfirmation. Deprecation and promotion require the last-read revision so stale\nrequests cannot overwrite newer work. An agent's authority claim is an instruction\ncontract, not a separate authentication system; the Unix account owns the data.\n\nSkills use YAML `name` and `description` metadata in `skills/<name>/SKILL.md`.\n`list_skills` returns descriptions, and `get_skill` loads the body on demand.\nA project/default skill overrides a global skill with the same name. Add\n`extends: global:NAME` to include the global skill's instructions before the local\ninstructions. The existing native skill-template system continues to work.\n\nSkill templates and their includes must stay under `global/skills/` or the active\nproject/default profile's `skills/` directory. Use config-root-relative paths such\nas `{% include \"global/skills/shared/checks.md\" %}`, or `./` paths relative to the\nincluding template. Nunjucks variables remain available. Symlinks are rejected,\nand each file is limited to 1 MiB. Move snippets and skill overrides stored\nelsewhere into these directories before rendering or loading those skills.\n\nThe installed `brain-memory`, `brain-consolidate`, `brain-review`, and `todo-manager`\nskills describe retrieval, persistence, consolidation, review learning, and task workflows. Review records use\nthe knowledge tools and remain inferred unless confirmed by the user.\n\n### Tasks and connectors\n\nTasks are separate from knowledge and stored in `todo/<id>.md`. Supported states\nare `todo`, `doing`, `blocked`, `done`, and `cancelled`. Tasks have titles,\ndescriptions, priorities, owners, due dates, labels, notes, and optional external\nsource identities.\n\n```sh\nagent-brain todo add --json '{\"scope\":\"project\",\"title\":\"Check refresh handling\",\"priority\":\"high\"}'\nagent-brain todo list\nagent-brain todo get ITEM_ID\nagent-brain todo complete ITEM_ID --revision REVISION\n```\n\nMCP exposes `todo_list`, `todo_get`, `todo_add`, `todo_update`, `todo_complete`,\n`todo_import`, and `todo_sync`. Update requests require the current revision.\n\nConfigure optional connectors in `brain.jsonc`:\n\n```jsonc\n{\n  \"enabled\": true,\n  \"connectors\": {\n    \"issues\": {\n      \"type\": \"github\",\n      \"repository\": \"my-org/my-project\",\n      \"tokenEnv\": \"GITHUB_TOKEN\"\n    },\n    \"board\": {\n      \"type\": \"trello\",\n      \"board\": \"BOARD_ID\",\n      \"keyEnv\": \"TRELLO_API_KEY\",\n      \"tokenEnv\": \"TRELLO_TOKEN\"\n    }\n  }\n}\n```\n\n```sh\nagent-brain todo import issues --scope project\nagent-brain todo sync issues --scope project\n```\n\nCredentials are read from the process environment and never written to task files.\nSet credentials in the service's environment.\nGitHub imports paginate and exclude pull requests. Trello maps due-complete cards\nto done, archived cards to cancelled, and other cards to todo; it does not guess\nworkflow states from list names.\n\nImports deduplicate by source identity and scope. Synchronization compares local\nand remote fields against the last imported version, preserves local-only edits,\nand reports conflicting task IDs without replacing those tasks. Deleted remote\nitems are retained locally. These connectors only read remote systems; completing\na local task does not close a GitHub issue or modify a Trello card.\n\n### Git portability\n\n```sh\nagent-brain sync status   # Preview Git status and eligible files\nagent-brain sync init     # Initialize the configuration Git repository\nagent-brain save          # Commit local brain changes and push\nagent-brain pull          # Pull remote changes with rebase\nagent-brain push          # Push existing commits\nagent-brain sync          # Commit local changes, pull, then push\n```\n\nCommands need no `--confirmed` flag. Saving generates a commit message from the\nnumber of changed files; use `--message \"Your message\"` to override it. Output\nreports completed steps, including a local commit if a later pull or push fails.\nExisting `agent-brain sync save|pull|push` forms remain supported. Bare\n`agent-brain sync` now performs synchronization; use `sync status` for a preview.\n\nFrom an agent prompt, ask to \"save brain changes\" or \"sync brain\". The MCP `sync`\ntool accepts the same actions and an optional message, without a confirmation\nparameter. Agents still need a user request or standing authorization to sync.\n\nSaving includes Markdown knowledge, skills, tasks, project metadata, and `.gitignore`.\nIt also includes all regular files under each scope's `templates/` directory,\nincluding nested Nunjucks templates and supporting files. Template additions,\nedits, and deletions are synced; symlinks are rejected.\nIt excludes indexes, runtime state, secrets, `brain.jsonc`, and native agent\nconfiguration. Existing staged changes block a save. Configure the remote and\nupstream with normal Git commands using your existing credentials.\nBrain Git operations use `AGENT_RUN_REAL_PATH` when available, so agent-session\nGit guards do not intercept configuration sync.\nAfter cloning onto another machine, run `agent-brain init` to restore generated\nprofile markers and shared templates, then update source roots in `config.yaml`\nto match that machine.\n\nThe configuration directory must itself be the repository root. Pull uses rebase\nand reports conflicted files; resolve the rebase before syncing again. Sync stops\non failure without pushing. Commands apply across all scopes in the configuration\nrepository, not just the current code project. Background commits and pushes are\nnot performed; the service can optionally pull at startup as described below.\n\n### Persistent service under apicore-server\n\nAll native agents connect to the same long-lived service for the current user.\nStart it on Linux, macOS, or Windows:\n\n```sh\nagent-brain serve\n```\n\nThe service hosts SDK Streamable HTTP at `/mcp` using apicore's Fastify instance.\nIt listens on `<config-root>/runtime/agent-brain.sock`, which defaults to\n`~/.agent-run/runtime/agent-brain.sock`. Both the service and clients use the\nconfigured root regardless of their environment. The socket\ndirectory must belong to the current user and have mode `0700`; the socket has\nmode `0600`. No TCP listener or application user database is created.\n\nGenerated native-agent configurations run `agent-brain mcp` through `PATH`, so\n`agent-brain` must be installed and available there. The bridge selects the socket\nwhen it starts; generated files do not depend on the installation or runtime\ndirectory used to render them. Re-render existing profiles with `agent-run update`\nto replace older commands that contain absolute installation paths. After\nupgrading from a version that used a different socket location, restart the service and\nagent sessions so they use the socket under the configuration root.\n\n`agent-run mcp` also bridges native-agent stdio to this socket. Use `--socket PATH`\nfor a particular service. The bridge verifies the socket's ownership and private\npermissions. A missing or unreachable socket is an error; start the service\nbefore connecting. There is no standalone stdio server or TCP fallback. Apicore\nsupports Unix sockets directly, so localhost binding is unnecessary. The brain\nservice supports Linux, macOS, and native Windows.\n\nOn Windows the default endpoint is `\\\\.\\pipe\\agent-brain-<hash>`, derived from\nthe user's home and configuration root. No TCP port is opened. Windows\nPowerShell applies a private pipe ACL before requests are accepted; each bridge\nchecks the pipe owner and ACL before connecting. `--socket` can select another\nlocal named pipe. Windows removes the pipe automatically when its server exits.\n\nTo start it automatically at Windows sign-in, initialize the desired config root\nand run the packaged installer in PowerShell:\n\n```powershell\nagent-brain init --configdir \"$env:USERPROFILE\\.agent-run\"\n$prefix = npm.cmd prefix -g\n& \"$prefix\\node_modules\\@technomoron\\agent-run\\scripts\\install-windows-brain.ps1\" -ConfigRoot \"$env:USERPROFILE\\.agent-run\"\n```\n\nThe `Agent Brain` scheduled task runs hidden as the signed-in user, without\nelevation, and retries failures. Its log is `<config-root>/runtime/service.log`.\nAfter upgrading the package, restart it with `Stop-ScheduledTask` followed by\n`Start-ScheduledTask` for task name `Agent Brain`.\n\nAfter a crash, remove a stale socket only after checking that its service is\nstopped. Starting a second service on an existing socket fails without replacing\nthe first service's socket.\n\nFor a user service, copy `ops/systemd/agent-brain.service` to\n`~/.config/systemd/user/` and adjust `ExecStart` if your executable is elsewhere.\nAdd `--configdir PATH` to `ExecStart` if you use a custom configuration root.\nRun `systemctl --user daemon-reload` followed by\n`systemctl --user enable --now agent-brain`. Installation is explicit.\n\nThe supplied service uses `serve --pull`. On startup this pulls the configuration\nrepository with `--ff-only --no-rebase` when it is clean and has an upstream.\nDirty checkouts and missing upstreams are skipped. Divergence or network failures\nare reported in the service journal and the service continues with local files.\nStartup never commits, pushes, stashes, or rebases local work. Omit `--pull` to\ndisable this behavior for a manually launched service.\n\nThe AI tools updater can install and restart the service for explicitly selected\naccounts; see [Systemd Jobs](#systemd-jobs). Existing user unit\noverrides still take precedence over the installed system-wide user unit.\n\nEach HTTP request resolves the proxy's source directory through agent-run's\nresolver. Tools cannot select another project's scope through arguments. The\nservice shares canonical files and the SQLite index; it does not keep a watcher\nor a separate authoritative cache.\n\n### Remaining roadmap\n\nThe initial implementation uses lexical retrieval and path matching. Embeddings,\nvector ranking, background watchers, debounced automatic Git synchronization,\nremote task writes, and additional connectors remain future work. No model\nprovider or external account is required for the local features.\n\nTransport and connector implementations follow the\n[Node MCP SDK server documentation](https://ts.sdk.modelcontextprotocol.io/server),\n[GitHub Issues REST API](https://docs.github.com/en/rest/issues/issues), and\n[Trello board API](https://developer.atlassian.com/cloud/trello/rest/api-group-boards/).\n\n## Systemd Jobs\n\nThe repo includes optional systemd units for keeping global AI tooling current.\nRun the installer from the agent-run checkout. Setup, generation, and updates do\nnot copy systemd units or helper scripts into `.agent-run`. Remove legacy copies\nthere once any custom changes have been moved to your maintained scripts.\n\nInstall the global AI tools updater:\n\n```sh\nsudo scripts/install-systemd-jobs.sh --ai-tools\n```\n\nThis installs and enables `ai-tools-update.timer`, which runs hourly. The\nupdater uses `/usr/local/bin/npm`, `/usr/local/bin/node`, and\n`/usr/local/bin/pnpm`, keeps global Node packages under `/usr/local`, and does\nnot delete command shims during recurring runs. It updates this fixed list of\nNode packages with npm:\n\n```text\nnpm, pnpm, corepack, fallow, ripgrep, pm2, tsx, typescript,\n@openai/codex, @anthropic-ai/claude-code, @google/gemini-cli,\n@xai-official/grok, and @technomoron/agent-run\n```\n\nThe updater clears inherited `SUDO_USER` for its root-owned pnpm configuration\nwrites, so it works both under sudo and from a root shell. It explicitly allows\nthe Claude, Grok, esbuild, and pnpm install hooks. Optional native build hooks\nsuch as keytar and node-pty remain subject to npm's script policy; the updater\ndoes not enable native compilation or require a working node-gyp installation.\n\nThe optional apt package list still defaults to `gh` and can be changed with\n`AI_TOOLS_APT_PACKAGES`.\n\nTo keep agent-brain running for a particular account, put\n`AI_TOOLS_BRAIN_USERS=\"bjorn\"` in `/etc/default/ai-tools-update`. The installer\nalso installs the user service and its management helper. After installing the\npackage, the updater enables that account's service, enables lingering so it\nstarts at boot without an interactive login, and restarts it to load the update.\nNo accounts are selected by default. The service remains owned by the selected\nuser and listens on that user's private Unix socket.\n\nNode 24 or newer must be installed at `/usr/local/bin/node` before running the\nupdater. `AI_TOOLS_AGENT_RUN_PACKAGE` can select a package version or a\nroot-owned local package archive while testing an unpublished build; it defaults\nto `@technomoron/agent-run@latest`. The updater's `--agent-brain` option installs\nonly this package and manages the selected services. The settings file is read\nby the systemd job; when invoking the script directly, pass these environment\nvariables explicitly.\n\n## Login Warning\n\nFor user-owned machines, `scripts/agent-config-login-warning.sh` can be called\nfrom a shell startup file to print a large warning when `~/.agent-config` is a\ndirty git checkout:\n\n```csh\nif ( -x \"$HOME/bin/agent-config-login-warning\" ) then\n    \"$HOME/bin/agent-config-login-warning\"\nendif\n```\n\nThe helper only reads the git status and exits quietly when the checkout is\nclean or absent. Set `AGENT_CONFIG_TARGET` before calling it to check a\ndifferent config tree.\n\n## Install\n\n```sh\nnpm install -g @technomoron/agent-run\n```\n\n## Release\n\nReleases publish from GitHub Actions, not from a local `npm publish`.\n\nAfter updating `package.json` and `CHANGES`, run:\n\n```sh\npnpm release\n```\n\nThis creates the annotated tag matching the package version and pushes that tag\nto `origin`. It stops if the tag already exists, and removes the local tag again\nif the push fails. The tag push triggers the release workflow, which runs the\ntests and build, packs, publishes to npm, and creates the GitHub release.\n\n`pnpm run release:preflight` is the local gate to run first: a clean build and\nthe full test suite. Update `package.json` and `CHANGES` yourself; nothing\nchecks them for you.\n","readmeFilename":"README.md"}