> ## Documentation Index
> Fetch the complete documentation index at: https://docs.prbe.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# Command reference

> Every probe command group and subcommand, with what it does.

Run `probe <group> --help` for the flags on any of these.

## Setup and account

> [!NOTE]
>
> **Setting the device up is the wizard's alone**: installing, updating, signing in and out, switching accounts and who records all go through `probe wizard` (or `npx probe-research`), at a keyboard or [as flags](/wizard/flags.md). The commands below read state or manage tokens. The full map is on [the wizard overview](/wizard/overview.md).

| Command | Does | In the wizard |
| - | - | - |
| `probe wizard` | The [setup wizard](/wizard/overview.md): install, update, sign in and out, accounts, uninstall | — |
| `probe doctor` | Read-only diagnostic: what is installed, on, and whether auto-update works. `--fix` turns retired folder defaults into `.probe.config` files | **Diagnose a problem** |
| `probe whoami` | The current principal | the **On this device** block |
| `probe context` | `list` · `show` · `use` · `delete` — named local accounts | **Account** switches and removes them |
| `probe token` | `list` · `create` · `revoke` | none — minting needs a browser |
| `probe mcp` | `status` · `headers` · `env` · `token set` · `token unset` | the read token is minted at sign-in |
| `probe feedback send` | Send the Probe team feedback about Probe. Nothing is sent until you say yes | — |

## Structure

| Command | Does |
| - | - |
| `probe workspace` | `list` · `get` · `create` · `rename` · `delete` · `use` · `writers`. `use` sets this computer's workspace, where new projects made here go |
| `probe project` | `create` · `list` · `get` · `set` · `use` · `tag` · `move` · `delete` · `lineage` · `reference` · `code` · `contributors` |
| `probe experiment` | `create` · `fork` · `get` · `set` · `list` · `move` · `freeze` · `reproduce` · `inherited` · `edges` · `lineage` · `delete` |
| `probe group` | `create` · `list` · `get` · `set` — sweeps, ensembles, distributed runs |
| `probe version` | `create` · `list` — immutable experiment version manifests |
| `probe access-group` | `list` · `create` · `rename` · `delete` · `add` · `remove` |
| `probe commits` | One page of a project's commit timeline, newest first |

`probe project delete`, `probe experiment delete` and `probe run delete` move what they delete to a trash that Probe support can restore for 21 days. `--dry-run` prints what would move, and moves nothing.

## Runs

| Command | Does |
| - | - |
| `probe run` | `start` · `fork` · `child` · `set` · `move` · `list` · `tag` · `expect` · `end` · `check` · `reproduce` · `get` · `series` · `metrics` · `inputs` · `upstream` · `delete` |
| `probe exec` | Run a command under a run, holding it with a heartbeat. `--input` / `--output` name the files a non-Python step reads and writes, so they are hashed for lineage |
| `probe get` | Print a run |
| `probe bundle` | Print a run bundle: run, series and artifacts |
| `probe events` | Backend lifecycle events for a run |
| `probe link` | Attach foreign keys under `metadata.foreign_keys` |

`probe run expect` declares the range a metric should stay in, and Probe emails the run's creator the first time a value leaves it. `probe run inputs` lists the files a run read; `probe run upstream` walks back to what it built on.

## Telemetry

| Command | Does |
| - | - |
| `probe log` | Append metric points. `--dim` adds series dimensions |
| `probe metrics` | `grouped` · `wide` · `export` · `plot` · `backfill` · `delete` |
| `probe series` | `latest` — cross-run scalar summary |
| `probe coordinates` | The run's coordinate catalog |
| `probe views` | `list` · `show` · `create` · `preview` · `data` · `rename` · `update` · `delete` |
| `probe span` | `add` · `list` · `get` |
| `probe trial` | `list` · `get` · `set` · `add` · `stage` · `reconcile` · `export` · `drain` · `watch` · `expand` |
| `probe edge` | `add` · `remove` — lineage |

## Files

| Command | Does |
| - | - |
| `probe artifact` | `add` · `list` · `tree` · `move` · `download` · `versions` · `version-add` · `pin-impact` · `gc-uploads` · `delete` |
| `probe shared` | `list` · `download` · `delete` — the older team files are read-only. `add` · `share` · `unshare` are still in the CLI, but the server refuses them (410): new team data goes in as a [dataset](/tracking/datasets.md) |
| `probe dataset` | `add` · `use` · `list` · `show` · `download` — the team's [datasets](/tracking/datasets.md) |
| `probe source` | `add` · `list` · `show` — where outside data came from |
| `probe checkpoint` | `list` · `use` — every checkpoint, team-wide |
| `probe provenance` | Where a dataset or checkpoint came from (`--down`: what used it; `--steps`: the methods section) |
| `probe file preview` | A local data file's shape and first rows (CSV, JSON, Parquet, NumPy), without running anything. Never opens a pickle |
| `probe snapshot` | Non-disruptive code and environment capture |
| `probe snapshot-show` | The captured code manifest, one file per line |
| `probe snapshot-restore` | Rebuild the captured tree, or say exactly what is missing |
| `probe snapshot-prune-refs` | Delete the `refs/probe/snapshots/*` git refs that earlier Probe versions wrote |

## Prose

| Command | Does |
| - | - |
| `probe summary` | `checkout` · `push` — a project's or experiment's summary (its Overview page) as a local file: check it out, edit it, push it. A push onto a page that moved meanwhile merges. See [Summaries](/tracking/summaries.md) |
| `probe visuals` | `options` · `set` — the tables and charts of a project's or experiment's Metrics center. `options` writes the current list and what it may name to a file; `set` sends the edited list |
| `probe draft edit` | Replace one exact piece of a checked-out summary or note draft. The change comes on stdin |
| `probe notes` | `show` · `checkout` · `push` · `write` · `append` · `edit` · `list` · `create` · `rename` · `delete` · `status` · `team` · `sync` · `audit-advisory` |
| `probe paper` | `add` · `list` · `update` · `tag` · `edges` · `remove` · `citations` · `graph` · `find` |
| `probe agent-rules` | `refresh` — the managed Probe block in your agent's memory file |

`probe paper find` searches and reads 40M+ abstracts (arXiv, PubMed, bioRxiv, medRxiv): `--mode read --paper-id arxiv:<id> --query "<question>"` returns the passages of one paper that answer a question.

## Sessions

| Command | Does |
| - | - |
| `probe session` | `state` · `track` · `untrack` · `toggle` · `status` · `default` · `parent` · `export` |
| `probe statusline` | `install` · `uninstall` · `status` · `show` — Install adds it, Uninstall removes it |
| `probe ignore check` | A path's [`.probe.config`](/agents/probe-config) level and the line that set it |

`probe session default` shows or sets the machine's default for new sessions (`on`, `read` or `off`). `probe session export <id>` prints a captured session as one ATIF trajectory document, readable by Harbor, Phoenix and Transluce.

## The Probe daemon

See [The Probe daemon](/agents/daemon.md).

| Command | Does |
| - | - |
| `probe ask "<question>"` | Ask the daemon about the team's prior work. Returns at once; the answer arrives later as a `[Probe]` message. `--wait` waits for it; `--writer` asks the daemon's writer to change the record |
| `probe approvals` | The questions the daemon is holding for you, answered y/n in a terminal (`--list` only lists), then the shell commands it ran on Jev's yes in the last day |
| `probe deny <id>` | Say no to a question the daemon holds. `--why` says why |
| `probe daemon status` | Whether the daemon can run here, and what it is doing |
| `probe daemon install` | Install the daemon's AI libraries into this CLI's environment |
| `probe companion` | `log` · `trace` · `report` · `feedback` — every decision the daemon made in a session and why, what it sent its model, what it wrote, and a correction it reads on its next cycle |

## Capy

Capy keeps no transcript on your computer, so its threads are captured through Capy's API. The installer runs `connect` when you pick Capy (`npx probe-research install --agent capy`). See [Capy](/agents/capy.md).

| Command | Does |
| - | - |
| `probe capy connect` | Start capturing the Capy threads you start: takes your Capy key and projects, asks for one browser approval, and installs a timer that syncs every 10 minutes |
| `probe capy sync` | Pull your new Capy messages and upload them now. `--quiet` prints only problems; the timer uses it |
| `probe capy status` | What is connected, and how the last sync went |
| `probe capy disconnect` | Remove the timer, the key, the sync record and the capture credential. `--keep-capture` keeps the credential |
| `probe capy setup` | Print the one step that puts Probe inside Capy: add the Probe plugin (its MCP server and skills) |

Flags for `probe capy connect`:

| Flag | Effect |
| - | - |
| `--project <name or id>` | A Capy project to capture. Repeat it for more. Required when not at a terminal |
| `--api-key-stdin` | Read the Capy key from stdin. Without it, the key comes from `$CAPY_API_KEY`, else a hidden prompt. Never pass the key as an argument: shell history keeps it |
| `--no-timer` | Do not install the timer |
| `--no-sync` | With `--no-timer`: do not sync right away |
| `--no-browser` | Print the approval link instead of opening it |

## Imports

> [!NOTE]
>
> These run in the foreground and hold the terminal. The wizard's **Import research work** runs the same imports in the background, survives a disconnect, and resumes after a restart — prefer it for anything large. See [Backfill](/integrations/backfill.md).

| Command | Does |
| - | - |
| `probe backfill` | Import work you have already done: point an agent at a folder. `--review-excluded` re-checks files an earlier import left out as not research |
| `probe wandb` | `discover` · `import-local` · `import-hosted` · `key` |
| `probe import wandb <entity/project/run_id> --run <run>` | Mirror one W\&B run's metric history into an existing run |

## Delivery

| Command | Does |
| - | - |
| `probe outbox` | `status` · `drain` · `watch` · `retry` · `discard` · `pause` · `resume` |
| `probe flush` | Deliver everything queued and wait (alias of `outbox drain`) |
| `probe sync` | Deliver runs recorded with `PROBE_MODE=offline`, with the current sign-in |

> **[The outbox](/cli/outbox.md)**
>
> What queues, what blocks, and what to do when delivery fails.


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