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

# CLI Commands

> Complete reference for all Feynman CLI commands, workflow commands, and flags.

This page covers every Feynman CLI command and flag. Research workflow commands like `feynman deepresearch` are also documented in the [Slash Commands](/reference/slash-commands) reference, since they map directly to REPL slash commands.

## Core commands

| Command                 | Description                                                 |
| ----------------------- | ----------------------------------------------------------- |
| `feynman`               | Launch the interactive REPL                                 |
| `feynman chat [prompt]` | Start chat explicitly, optionally with an initial prompt    |
| `feynman help`          | Show CLI help                                               |
| `feynman setup`         | Run the guided setup wizard                                 |
| `feynman doctor`        | Diagnose config, auth, Pi runtime, and preview dependencies |
| `feynman status`        | Show the current setup summary (model, auth, packages)      |

<Tip>
  Run `feynman setup` first on a new machine. Feynman will also auto-launch setup if no model is configured and stdin is a TTY.
</Tip>

## Model management

| Command                              | Description                              |
| ------------------------------------ | ---------------------------------------- |
| `feynman model list`                 | List available models in Pi auth storage |
| `feynman model login [id]`           | Login to a Pi OAuth model provider       |
| `feynman model logout [id]`          | Logout from a Pi OAuth model provider    |
| `feynman model set <provider/model>` | Set the default model for all sessions   |

The `model set` command writes the new default to `~/.feynman/settings.json`. The format is `provider/model-name`:

```bash theme={null}
feynman model set anthropic/claude-sonnet-4-5
feynman model set openai/gpt-5
```

To see all models you have configured and their authentication status:

```bash theme={null}
feynman model list
```

## AlphaXiv commands

| Command                | Description                |
| ---------------------- | -------------------------- |
| `feynman alpha login`  | Sign in to alphaXiv        |
| `feynman alpha logout` | Clear alphaXiv auth        |
| `feynman alpha status` | Check alphaXiv auth status |

AlphaXiv authentication enables Feynman to search and retrieve papers, access discussion threads, and pull citation metadata. Once authenticated, the `alpha` tools are available inside the REPL for paper search, Q\&A, and code inspection.

## Package management

| Command                             | Description                                                   |
| ----------------------------------- | ------------------------------------------------------------- |
| `feynman packages list`             | Show core and optional Pi package presets with install status |
| `feynman packages install <preset>` | Install an optional package preset                            |
| `feynman update [package]`          | Update installed packages, or a specific package by name      |

Use `feynman packages list` to see which optional packages are available and which are already installed. Pass a specific package name to `feynman update` to update only that package. See [Packages](/reference/packages) for the full list of presets.

```bash theme={null}
feynman packages install generative-ui
feynman update
feynman update pi-subagents
```

## Utility commands

| Command                 | Description                               |
| ----------------------- | ----------------------------------------- |
| `feynman search status` | Show Pi web-access status and config path |

## Workflow commands

All research workflow slash commands can also be invoked directly from the CLI. Feynman translates them into the corresponding REPL slash command on launch:

| Command                        | Description                                                                                   |
| ------------------------------ | --------------------------------------------------------------------------------------------- |
| `feynman deepresearch <topic>` | Run a thorough, source-heavy investigation and produce a research brief with inline citations |
| `feynman lit <topic>`          | Run a literature review using paper search and primary-source synthesis                       |
| `feynman review <artifact>`    | Simulate an AI research peer review with likely objections, severity, and a revision plan     |
| `feynman audit <item>`         | Compare a paper's claims against its public codebase for mismatches and reproducibility risks |
| `feynman replicate <paper>`    | Plan or execute a replication workflow for a paper, claim, or benchmark                       |
| `feynman compare <topic>`      | Compare multiple sources and produce a source-grounded agreement/disagreement matrix          |
| `feynman draft <topic>`        | Turn research findings into a polished paper-style draft                                      |
| `feynman autoresearch <idea>`  | Autonomous experiment loop — try ideas, measure results, repeat                               |
| `feynman watch <topic>`        | Set up a recurring or deferred research watch on a topic                                      |

```bash theme={null}
feynman deepresearch "mechanistic interpretability in transformers"
feynman lit "diffusion models for protein folding"
feynman review outputs/my-paper.md
feynman audit 2401.12345
feynman replicate "GPT-4 MMLU benchmark"
feynman compare "LoRA vs full fine-tuning"
feynman draft "scaling laws for retrieval-augmented generation"
feynman watch "llm reasoning benchmarks"
feynman autoresearch "minimize bundle size of my webapp"
```

These are equivalent to launching the REPL and typing the corresponding slash command. The CLI form is useful for scripting and automation.

## Flags

| Flag                       | Description                                                            |
| -------------------------- | ---------------------------------------------------------------------- |
| `--prompt "<text>"`        | Run one prompt and exit (one-shot mode)                                |
| `--model <provider:model>` | Force a specific model for this session                                |
| `--thinking <level>`       | Set thinking level: `off`, `minimal`, `low`, `medium`, `high`, `xhigh` |
| `--cwd <path>`             | Set the working directory for all file operations                      |
| `--session-dir <path>`     | Set the session storage directory                                      |
| `--new-session`            | Start a new persisted session                                          |
| `--alpha-login`            | Sign in to alphaXiv and exit                                           |
| `--alpha-logout`           | Clear alphaXiv auth and exit                                           |
| `--alpha-status`           | Show alphaXiv auth status and exit                                     |
| `--doctor`                 | Alias for `feynman doctor`                                             |
| `--setup-preview`          | Install preview dependencies (pandoc)                                  |

### Thinking levels

The `--thinking` flag (and `FEYNMAN_THINKING` env var) controls how much extended reasoning the model applies before responding. Higher levels produce more thorough analysis at the cost of latency and token usage.

| Level     | Description                               |
| --------- | ----------------------------------------- |
| `off`     | No extended thinking                      |
| `minimal` | Minimal reasoning pass                    |
| `low`     | Light thinking                            |
| `medium`  | Default — balanced reasoning and speed    |
| `high`    | Deep reasoning for complex research tasks |
| `xhigh`   | Maximum reasoning budget                  |

```bash theme={null}
# One-shot mode
feynman --prompt "Summarize the key findings in outputs/my-brief.md"

# Force a model for one session
feynman --model anthropic/claude-opus-4-5 --thinking high

# Per-project session isolation
feynman --session-dir ~/projects/myproject/.sessions
```

<Note>
  `--model` accepts both `/` and `:` as separators (`anthropic/claude-sonnet-4-5` and `anthropic:claude-sonnet-4-5` are both valid).
</Note>