Command surface

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

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.

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.

Getting started

CLI

Homology search

Ontology

AI Foundry

Evals

Evidence namespaces

Query and semantics

Models, releases, and evaluation

Execution and storage

​Evidence namespaces

​Query and semantics

​Models, releases, and evaluation

​Execution and storage

Evidence namespaces

Query and semantics

Models, releases, and evaluation

Execution and storage