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Run experiments, capture\nevidence, search indexed sources, ask grounded questions, and let coding agents\ndrive Gateway without a separate transport.\n\n```bash\nnpm i -g @synsci/atlas\natlas login\natlas doctor\natlas init\n```\n\nThat's the entire setup. `atlas login` opens a browser, redeems a Gateway API\nkey, and writes it to the local profile config. `atlas doctor` checks auth,\nbackend reachability, integration freshness, and bundled skills. `atlas init`\nfind-or-creates the project for the current repo/folder and writes `atlas.json`,\nthe opt-in activation contract for ambient research behavior.\n\nWhen `atlas.json` is present, coding agents can stay mostly invisible while\nstill adding value: load `atlas brief` when context matters, auto-scope\n`library:*` to project sources, use `web:*` as a Gateway-metered search/fetch\npath, and append compact breadcrumbs with `log:*`. If Gateway is unavailable,\nunauthenticated, over quota, or not relevant, agents should fail open and keep\nworking normally.\n\n## What it looks like\n\nGateway now renders human-friendly output by default when you're at a terminal.\nPipe the same command and you get JSON for scripting.\n\n```text\n$ atlas key:list\n NAME PREFIX CREATED LAST USED STATE\n─ ──────────────────────────────── ──────────── ─────── ───────── ───────\n● atlas-cli thk_856dc108 3d ago just now active\n● synsci · darwin · Aayams-MacBoo… thk_d41ccc8e 3d ago 17h ago active\n· old-key thk_28a2d4a0 7d ago 8d ago revoked\n\n2 active · 1 revoked\n\n$ atlas library:list\nID STATUS TYPE NAME UPDATED\n──────── ─────────── ─────────────── ──────────────────────────────── ───────\ndded7078 ● completed documentation ModalDocs 1mo ago\nd36f499b ● completed research_paper GShard: Scaling Giant Models… 1mo ago\ne3ea6910 ● error research_paper Attention Is All You Need 1mo ago\n\n3 sources · 1 errored (atlas library:retry to re-run)\n```\n\nForce a format with `--format=json|tsv|csv|table|pretty`. Set\n`default_format` in your profile with `atlas config:set` to make it sticky.\n\n## Quick reference\n\n### Look at what's there\n\n```bash\natlas project:list # find a project root (slug or UUID)\natlas log:tail # recent project research-log entries\natlas node:list # every node you can see\natlas library:list # every indexed source\natlas key:list --active-only # API keys, only the live ones\natlas usage:summary # quota usage for the current billing period\natlas integrations:status # github / wandb / huggingface connections\n```\n\n### Drill in\n\n```bash\natlas node:show --node able-helm-1359 # slugs work everywhere\natlas map:summary --node able-helm-1359 # rendered map summary\natlas map:tree --node able-helm-1359 --max-depth 3\natlas exec:list --node able-helm-1359\natlas evidence:list --node able-helm-1359\n```\n\n`--node` is an alias for `--node-id`; `--project` for `--project-id`. Slugs\n(`able-helm-1359`) and UUIDs both work — the CLI resolves slugs automatically\nvia `/nodes/resolve-by-slug` before dispatch.\n\n### Write\n\n```bash\natlas log:append --title \"why we changed the eval\" --body @note.md\natlas note:add --project able-helm-1359 --text @notes.md\natlas run:record --project able-helm-1359 \\\n --title \"lr=3e-4 seed=17\" \\\n --config-json '{\"lr\":3e-4,\"seed\":17}' \\\n --metrics-json '{\"val_loss\":2.31}' \\\n --outcome success\natlas node:create --payload-json @new-node.json\natlas evidence:add --node able-helm-1359 \\\n --items '[{\"local_path\":\"report.md\",\"artifact_type\":\"text\"}]' \\\n --expected-revision 4\n```\n\n### Compare runs\n\n`run:compare` renders a matrix across runs in a project. Columns can be node\nfields *or dot-paths into the run data* (`config.lr`, `metrics.val_loss`):\n\n```bash\natlas run:compare \\\n --root able-helm-1359 \\\n --cluster resnet50/cifar10/lr-sweep \\\n --columns title,config.lr,metrics.val_loss,outcome \\\n --format=table\n```\n\nPair with `--run-cluster-key` on `run:record` so identically-shaped\nexperiments fold into one comparable axis.\n\n### Ambient search/fetch\n\n```bash\natlas library:search --query \"windowed attention with global tokens\"\natlas web:search --query \"latest ARC-AGI public leaderboard\" --num-results 5\natlas web:fetch --url https://example.com/paper\n```\n\nInside an `atlas.json` project, `library:*`, `web:*`, and `log:*` auto-fill the\nproject/source context where possible. The web commands are intended as a\nprovenance-capturing alternative to ad hoc WebSearch/WebFetch when the result\nshould belong to the project.\n\n### Optimize an artifact (GEPA loop)\n\nWhen there's a single artifact and a quantitative benchmark, hand the\ntuning to GEPA — every candidate lands in the map with lineage, a\nper-example scorecard, the exact commit, and a live budget on the\ncontrol node:\n\n```bash\natlas optimize:start \\\n --target prompts/classify.txt \\\n --benchmark \"python eval.py --candidate {target}\" \\\n --objective \"maximize spam F1 on the holdout set\" \\\n --gate \"pytest tests/core -x\" --ground --parallel 4\n\natlas optimize:status --node # budget, best, stall\natlas optimize:stop --node # graceful mid-run stop\natlas run:chart --project --metric metrics.score\n\n# Before claiming a result, referee it: N replications at the candidate's\n# exact commit, mean/std + one-sided t-test, referee-report node.\natlas optimize:verify --node \\\n --benchmark \"python eval.py --candidate {target}\" \\\n --seeds 10 --threshold 0.9 --metric max\n```\n\n`--parallel K` evaluates K candidates concurrently; `--resume `\ncontinues a campaign from its best recorded candidate. `--ground` consults\nyour indexed library when the search stalls and folds the answer into\nGEPA's reflection. Requires `uv` + a reflection-LM key.\nAlready running gepa yourself? Add the bundled `AtlasCallback` (see the\n`atlas-optimize` skill) to stream any run into the map — one line.\n\n### Search and ask\n\n```bash\natlas library:add --type research_paper --url https://arxiv.org/abs/1706.03762\natlas library:search --query \"windowed attention\"\natlas library:ask --query \"what does Switch Transformer route on?\"\natlas research:ask --query \"compare MoE routing across recent papers\"\natlas library:retry --source-id # re-trigger a stuck index\n```\n\n### Capture code\n\n```bash\natlas github:link # connect your GitHub account\natlas repo:capture --node able-helm-1359 \\\n --repo-url \"$(git remote get-url origin)\" \\\n --branch-name \"$(git rev-parse --abbrev-ref HEAD)\" \\\n --head-commit-sha \"$(git rev-parse HEAD)\" \\\n --pin true\n```\n\n`repo:capture` records the exact code state behind a node. `--pin` creates an\nimmutable tag on the repo so a public-graph viewer can always re-open the\nexact commit; pins persist into the node's code-state and travel with\n`node:branch`, `map:export`/`import`, and `fork`. `atlas reproduce --node \n--check` prefers the pinned tag and fails when the commit is not reachable on\nthe remote.\n\n### Share and fork graphs\n\nSharing is graph-scoped: visibility and collaborators live on the **project\nroot**, and every descendant inherits them — child nodes have no separate\nvisibility.\n\n```bash\natlas node:share --node --visibility public # private | unlisted | public\natlas access:set --node # viewer | editor | admin collaborators\natlas fork --node # copy a visible graph into your account\n```\n\n`atlas fork` copies any visible node/subtree into your account as a new private\ngraph, preserving code-state and provenance — browse a public graph, then fork\nand continue from it. No export/import dance.\n\n### Install bundled skills into your coding agent\n\n```bash\natlas install # interactive picker (Claude Code, Cursor, Codex,\n # Windsurf, Aider, Continue, Goose)\natlas install --dry-run # print the plan first\natlas install --agent=claude-code,cursor # non-interactive\natlas install --no-hooks # skills only, skip the ambient logging hook\natlas install --uninstall # cleanly remove (skills + hooks)\n```\n\nOn Claude Code and Cursor, `atlas install` also wires a post-tool hook\n(matcher `WebSearch|WebFetch`) that records the agent's web activity to the\nproject research log automatically — a strict no-op outside an `atlas.json`\nproject, and respecting `auto.enabled`/`auto.log`. This is the deterministic\nhalf of the ambient layer: provenance without the agent having to remember to\ncall Gateway. `--no-hooks` opts out; `--uninstall` removes it cleanly.\n\nSymlinks where the agent reads a directory of `SKILL.md` files (Claude Code).\nWhole-file adapter for Cursor/Aider/Continue/Goose. Managed block inside\nCodex `AGENTS.md` and Windsurf `global_rules.md` — pre-existing content\noutside the markers is preserved exactly.\n\n### Profiles, keys, secrets\n\n```bash\natlas whoami # email, name, key prefix\natlas config:set --base-url # point at a different environment\natlas config:list # all local profiles\natlas key:create --name \"ci-runner\" # mint a new API key\natlas secrets:set < key.txt # store a key in macOS Keychain\n```\n\n## Output formats\n\n| Format | When | Notes |\n|-----------|------------------|-------|\n| `pretty` | TTY default | Per-command views (status glyphs, relative times, status footers). |\n| `json` | Pipe default | Lossless — every field, no truncation. Always available with `--format=json`. |\n| `table` | Opt-in | Same per-command views as `pretty`, without color. |\n| `tsv`/`csv` | Opt-in | One row per item; nested objects stringified. |\n\n```bash\natlas node:list # pretty when you're at a terminal\natlas node:list | jq '.nodes[0]' # json automatically when piped\natlas node:list --format=json # force json (always)\n```\n\n## Errors and discovery\n\nThe CLI translates raw backend responses into actionable messages and points\nat a discovery command when you forget a flag:\n\n```text\n$ atlas map:summary\n--node is required — try `atlas node:list` or pass a slug like `able-helm-1359`\n\n$ atlas note:add\n--project is required — try `atlas project:list` to find one\n\n$ atlas node:show --node bogus\nInvalid ID format (node:show). Gateway IDs are UUIDs — try `atlas node:list` to\nfind one, or pass a slug (e.g. able-helm-1359).\n```\n\n`atlas doctor` checks integration freshness too — expired GitHub tokens are\nsurfaced as warnings instead of pretending everything is OK.\n\n## Environment variables\n\n| Variable | Purpose |\n|----------|---------|\n| `ATLAS_API_KEY` | Override the stored API key for this invocation. |\n| `ATLAS_BASE_URL` | Point at a non-production API. |\n| `ATLAS_CLI_CONFIG_PATH` | Alternate profile config file. |\n| `NO_COLOR` / `FORCE_COLOR` | Disable / force ANSI color in `pretty` output. |\n| `ATLAS_LOGIN_TIMEOUT_MS` | Browser-login wait timeout (default 5 min). |\n\n## Command surface\n\nCommands are grouped by domain. The \"other\" catch-all is gone — every command\nlives in a real group:\n\n- **auth** · `login`, `logout`, `whoami`, `doctor`, `secrets:*`\n- **config** · `config:list`, `config:show`, `config:set`, `config:unset`\n- **account** · `account:update`\n- **setup** · `init`, `install`\n- **map** · `node:*`, `map:*`, `link:*`, `access:*`, `draft:*`, `label:*`, `project:list`, `program:snapshot`, `history:export`\n- **share** · `node:share` (graph-scoped visibility), `access:set/set-bulk` (viewer/editor/admin), `fork` (copy a visible public graph into your account)\n- **evidence** · `evidence:*`\n- **research-loop** · `brief`, `hypothesis:add/update`, `experiment:plan`, `decision:add`, `eval:define`, `reproduce`\n- **runs** · `run:record`, `run:compare`, `run:chart`, `run:spool:*`, `leaderboard` (managed executions: `exec:start/list/stop`)\n- **optimize** · `optimize:start`, `optimize:status`, `optimize:stop`, `optimize:verify`, `optimize:progress` (GEPA loop over an artifact, recorded into the map; verify = N-seed referee)\n- **journal** · `note:add`, `notebook:cell`, `log:*`\n- **integrations** · `github:*`, `integration:*`, `repo:capture`, `repo:pin`, `repo:push`\n- **keys** · `key:create`, `key:list`, `key:rotate`, `key:delete`\n- **library-research** · `library:*`, `web:*`, `research:*`, `usage:summary`\n- **agent** · `agent:run`\n- **ops** · `ops:maps:*` (admin)\n\n```bash\natlas help # text listing\natlas help # text help for one command\natlas help --schema --format=json # full request shape\natlas help --format=json # the full command catalog\n```\n\n## Skills\n\nNine bundled CLI-only Gateway skills ship in the package:\n\n| Skill | Use when the user wants… |\n|-------|--------------------------|\n| `atlas` | Base guidance + the skill router; map reading commands. |\n| `atlas-lab` | \"Log this run\" / \"continue the research\" — the loop: brief → hypothesis → plan → record → compare → decide. |\n| `atlas-frontier` | \"What's next?\" (plan-only) or \"keep going\" (autonomous, budgeted). |\n| `atlas-optimize` | \"Make this faster/better against a metric\" — the GEPA loop over one artifact. |\n| `atlas-autoresearch` | \"Prove it / publish it\" — refereed campaign: researchify → pre-register → search → verify → report. |\n| `atlas-map` | \"Turn this paper/repo into the map\" — source-to-nodes authoring. |\n| `atlas-search` | \"Search/ask our sources\" — library search, grounded Q&A, deep research. |\n| `atlas-reproduce` | \"Reproduce/validate this claim or result.\" |\n| `atlas-paper` | \"Turn this graph into a paper\" — draft a publication-style manuscript from graph claims, runs, evidence, sources, and code-state. |\n\n`atlas install` drops these into every coding agent on the machine.\n\n## Agent onboarding\n\nIf you want a coding agent to onboard a new user, paste this prompt:\n\n```text\nYou are an agent onboarding me to Gateway by Synthetic Sciences — the research map\nwhere my experiments, hypotheses, evidence, and decisions live permanently. Set\nit up end to end:\n\n1. `npm i -g @synsci/atlas@latest`, then `atlas login` and ask me to approve in\n the browser when it opens.\n2. `atlas doctor --format=json` — verify auth, backend, and the nine bundled\n skills (atlas, atlas-lab, atlas-frontier, atlas-optimize, atlas-autoresearch,\n atlas-map, atlas-search, atlas-reproduce, atlas-paper). Then `atlas install` to wire them\n into this agent.\n3. `atlas init` — bootstrap the project for this folder/repo (dedupe-safe,\n re-runnable) and write `atlas.json` so ambient Gateway behavior is opt-in to\n this project.\n4. `atlas brief --project ` — load the context packet and summarize it for\n me: open hypotheses, recent runs, failures, decisions, and suggested next.\n\nHouse rules: the skills are bundled in the CLI — never configure separate skill\ndownloads or legacy host transports. Commit code before recording runs (code\nstate is auto-captured onto every run). Never print my full API key into shared\nlogs — summarize the key prefix, storage location, CLI version, doctor result,\nand skill count when setup is complete.\n```\n\nAgents should inspect command metadata with `atlas help --format=json` and\nper-command request shapes with `atlas help --schema --format=json`.\n\n## Links\n\n- App: \n- Docs: \n- Issues: \n\nMIT licensed.\n","readmeFilename":"README.md"}