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

# Command surface

> Every rafflesia namespace, what it covers, and how to discover the full command tree without reading a list.

The command tree is discoverable from the CLI itself, which is the only listing
guaranteed to match the binary you have installed:

```bash theme={"dark"}
rafflesia --help
rafflesia proteins --help
rafflesia commands manifest --json
rafflesia commands namespaces --json
```

`commands manifest` returns the machine-readable registry — every primitive, its
operation id, and its request contract. It is the right input for an agent that
needs to plan against the surface rather than hard-code it.

## Evidence namespaces

| Namespace     | Covers                                                                                                                                                                  |
| ------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `refs`        | Resolve an identifier or free-text query into typed reference candidates.                                                                                               |
| `sequences`   | Records, catalogs, alignments, MSAs, profiles, and release search.                                                                                                      |
| `proteins`    | Structures, confidence, regions, residues, pockets, folds, interfaces, ligands, metals, disulfides, secondary structure, complexes, variants, dynamics, and validation. |
| `genomes`     | Assemblies, regions, intervals, and genome-coordinate variants.                                                                                                         |
| `annotations` | Source annotation fetches and annotation mappings.                                                                                                                      |
| `molecules`   | Import, inspect, fingerprints, descriptors, normalization, and similarity search.                                                                                       |
| `maps`        | Cryo-EM map metadata.                                                                                                                                                   |
| `simulations` | Simulation evidence.                                                                                                                                                    |

## Query and semantics

| Namespace                                  | Covers                                                                                   |
| ------------------------------------------ | ---------------------------------------------------------------------------------------- |
| `query run` / `explain` / `export`         | Release-pinned read-only SQL, preflight, and bounded exports.                            |
| `query databases` / `releases` / `sources` | Discover logical databases, immutable releases, and the relations each exposes.          |
| `query ontology`                           | Inspect and compose the immutable relation ontology, including paths and context slices. |
| `query joins` / `join-*`                   | Declared joins plus the measured evidence that authorizes a specific release pair.       |
| `query bql`                                | Compile and type-check Biology Query Language modules against the ontology.              |
| `query contract`                           | The pinned portable SQL dialect, limits, functions, and calibrated budgets.              |

## Models, releases, and evaluation

| Namespace                     | Covers                                                                            |
| ----------------------------- | --------------------------------------------------------------------------------- |
| `repositories`                | Model, dataset, and ontology repositories with their latest published releases.   |
| `registry`                    | Immutable registry releases, reconciliation receipts, and rebuild-drill evidence. |
| `datasets`                    | Dataset fan-out, source snapshots, and release history.                           |
| `environments`                | Immutable evaluation environments, releases, and tasks.                           |
| `episodes` / `rollout-groups` | Create, inspect, and group evaluation episodes; read their events and artifacts.  |

## Execution and storage

| Namespace                        | Covers                                                                       |
| -------------------------------- | ---------------------------------------------------------------------------- |
| `jobs`                           | Durable job submission and inspection.                                       |
| `objects`                        | Content-addressed object primitives.                                         |
| `artifacts` / `object-artifacts` | Paper artifact manifests and the object-backed artifact cache.               |
| `cache`                          | Cache measurement, admission, warming, and eviction.                         |
| `audit`                          | API audit log reads.                                                         |
| `system`                         | Build info, health, and infrastructure request records.                      |
| `commands`                       | Command introspection: the manifest and namespace listing.                   |
| `auth`                           | Login, logout, credential status. See [Authentication](/cli/authentication). |

<Note>
  Namespaces are stable; individual subcommands are added as primitives ship.
  When a script needs to assert the surface it depends on, pin against
  `rafflesia commands manifest --json` rather than a documentation table.
</Note>