# CLI Reference

This is the canonical reference for the implemented Notarius command-line
interface. For the shortest successful run, see the [README](../README.md).
Configuration fields, discovery rules, and selectable module keys are defined
in [Configuration](config.md); runtime state and recovery procedures are
defined in [Operations](operations.md).

## Command Summary

~~~
notarius help
notarius run <pipeline-id> --input path/to/source.json [--json] [flags]
notarius config validate [--config path/to/config.yml] [--pipeline pipeline-id] [--only lane-a,lane-b]
notarius pipelines list [--config path/to/config.yml] [--json]
~~~

Running Notarius without arguments, or with **help**, **--help**, or **-h**,
writes the command summary to standard output and exits with status 0.

## run

~~~
notarius run <pipeline-id> --input path/to/source.json [--json] [flags]
~~~

The **run** command executes the named pipeline for one input file. The
pipeline ID and **--input** are required.

| Flag | Meaning |
| --- | --- |
| **--config path** | Use this configuration file. When omitted, configuration discovery applies; see [Configuration](config.md). |
| **--input path** | Source input file to process. Required. |
| **--output-dir path** | Override the configured output root for this run. |
| **--json** | Write the successful run-result receipt as JSON to standard output. |
| **--chunk_cache auto\|bypass\|refresh** | Override chunk-plan cache handling for this run. |
| **--resume** | Reuse compatible recorded checkpoints when checkpoint recording is enabled. |
| **--recompute-step step-id** | With **--resume**, recompute the selected ordered step and its dependent lanes. It cannot be combined with **--only**. |
| **--debug** | Retain a debug bundle for this run. |
| **--debug-dir path** | Override the debug-bundle root. Requires **--debug**. |
| **--only lane-a,lane-b** | Run only the selected comma-separated artifact lanes when that selection is valid for the configured pipeline. |
| **--llm-profile id** | Highest-precedence configured profile for selected LLM-backed bindings and validators; it replaces binding and [pipeline](config.md#pipelines) defaults. |
| **--session-id id** | Supply a non-empty prompt session identifier to LLM-backed module calls. |
| **--reasoning-effort value** | Replace the selected PromptKit profile's reasoning effort for every LLM-backed call in this run. The value must be non-empty and the flag may be specified only once. |
| **--clear-reasoning-effort** | Clear reasoning effort inherited from the selected PromptKit profile for every LLM-backed call in this run. |
| **--reference selector=path** | Add or replace a file reference binding. Repeatable. |
| **--without-reference selector** | Remove a configured optional reference binding. Repeatable. |

**--chunk_cache** accepts only **auto**, **bypass**, or **refresh**.
**--debug-dir**, **--output-dir**, **--session-id**, and
**--reasoning-effort**, and **--recompute-step** reject explicit empty values.
**--reasoning-effort** and **--clear-reasoning-effort** are mutually exclusive.
When neither is present, reasoning effort comes from the selected PromptKit
profile. These controls apply to the shared run client, including retries and
LLM-backed validators, and do not modify configuration or profile files.
Persistent reasoning settings remain a PromptKit profile concern.
**--recompute-step** requires **--resume**; checkpoint requirements and reuse
behavior are documented in [Operations](operations.md).

### Reference selectors

Use **--reference** only for a reference slot declared by the selected
configured target. The accepted selector forms are:

| Form | Target |
| --- | --- |
| slot=path | The unique selected target that declares slot. |
| chunk.slot=path | The chunker. |
| merge.slot=path | The unique selected merger that declares slot. |
| lane.slot=path | The unique extractor, merger, or normalizer in lane that declares slot. |
| lane.extract.slot=path | The extractor in lane. |
| lane.merge.slot=path | The merger in lane. |
| lane.normalize.slot=path | The normalizer in lane. |

**--without-reference** uses the same selector forms without =path. Slot
names, requiredness, and configured bindings are part of the
[configuration contract](config.md).

### Run output

Without **--json**, standard output contains the completed pipeline ID, counts
of normalized and rejected outputs, and the output directory. A debug-enabled
run also prints its debug-bundle path to standard output. A successful run with
warnings reports the warning count to standard error. The published JSON bundle
is defined by the [JSON output contract](integrations/json-output.md).

With **--json**, successful standard output is exactly one
`notarius.run-result.v1` JSON document followed by a newline, with no
human-oriented status or debug-path line. Its fields and compatibility policy
are defined by the [run-result contract](integrations/run-result.md). A caller
must check for exit status 0 before decoding this output; a failed write can
leave incomplete standard-output bytes that are not a result document.

Example:

~~~
OPENROUTER_API_KEY=your-api-key \
  go run ./cmd/notarius run dnd-session \
    --config examples/dnd-minimal.config.yml \
    --input examples/seriatim-minimal-transcript.json
~~~

## config validate

~~~
notarius config validate [--config path/to/config.yml] [--pipeline pipeline-id] [--only lane-a,lane-b]
~~~

This command loads and validates a configuration. With **--pipeline**, it also
resolves that pipeline against the production module catalog. **--only** selects
lanes during that resolution and requires **--pipeline**.

Success is written to standard output as either config "<path>" is valid or
config "<path>" is valid for pipeline "<pipeline-id>".

Examples:

~~~
go run ./cmd/notarius config validate \
  --config examples/dnd-minimal.config.yml \
  --pipeline dnd-session

OPENROUTER_API_KEY=validation-placeholder \
  go run ./cmd/notarius config validate \
    --config examples/dnd-complete.config.yml \
    --pipeline dnd-session
~~~

The placeholder in the second command is sufficient only for offline
validation; it cannot run a provider-backed pipeline.

## pipelines list

~~~
notarius pipelines list [--config path/to/config.yml] [--json]
~~~

This command lists configured pipeline IDs in sorted order. By default, it
writes one ID per line to standard output. **--json** writes an object shaped as
{"pipelines":[...]} instead.

~~~
go run ./cmd/notarius pipelines list \
  --config examples/dnd-minimal.config.yml
~~~

## Output Streams And Exit Statuses

Successful commands write their primary result to standard output. Warnings and
errors are written to standard error.

For **run --json**, warnings remain on standard error and standard output is a
machine-readable success result only. Syntax and runtime diagnostics remain on
standard error. Parse the result only after the process exits with status 0.

| Status | Meaning |
| --- | --- |
| 0 | The command completed successfully, including root help. |
| 1 | Command syntax was valid but configuration loading or validation, pipeline resolution or execution, provider use, output, or requested debug handling failed. |
| 2 | The command or flag syntax was invalid, including unknown commands, missing required arguments, invalid flag values, or invalid flag combinations. |

The root help spellings are the supported help path. Invoking **--help** on
**run**, **config validate**, or **pipelines list** is handled by the flag
parser as a usage error: it writes an error to standard error and exits with
status 2.