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notarius/docs/cli.md

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# CLI Reference
This is the canonical reference for the implemented Notarius command-line
interface.
For the minimal end-to-end invocation, see the [README](../README.md).
## Commands
```text
notarius help
notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b] [--chunk_cache auto|bypass|refresh] [--output-dir path] [--resume] [--debug [--debug-dir path]] [--llm-profile id] [--session-id id] [--reference selector=path] [--without-reference selector]
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` with no arguments, `notarius help`, `notarius --help`, or
`notarius -h` prints usage and exits successfully.
## `run`
`notarius run <pipeline-id>` executes a configured pipeline against one input
file.
Flags:
- `--input path`: required source input file.
- `--config path`: config file path. If omitted, Notarius uses the discovery
rules in [Configuration](config.md#discovery).
- `--only lane-a,lane-b`: run only the named artifact lanes. Values are
comma-separated and must be non-empty.
- `--resume`: request checkpoint reuse for this invocation. See
[Operations](operations.md#checkpoint-cache) for prerequisites and reuse
behavior.
- `--chunk_cache auto|bypass|refresh`: select chunk-plan reuse for this
invocation. `auto` reuses a valid plan by canonical source digest, `bypass`
performs no plan-cache I/O, and `refresh` regenerates and replaces a valid
plan only after chunk validation succeeds. See
[Configuration](config.md#state-surfaces) for the persistent setting, precedence,
and cache-root selection.
- `--output-dir path`: output root. Defaults to `./notarius-output`.
- `--debug`: allocate and retain one debug bundle for this invocation.
- `--debug-dir path`: debug-bundle root override. This flag requires `--debug`.
- `--llm-profile id`: override every effective LLM-capable pipeline module
binding with one Scriptorium profile ID. Validator-specific profiles are not
overridden.
- `--session-id id`: pass a stable prompt session identifier through LLM-backed
module calls.
- `--reference selector=path`: bind a reference path to a chunk, extractor,
merger, or normalizer reference slot. Repeatable.
- `--without-reference selector`: remove a configured optional reference binding.
Repeatable. It accepts the same selector forms as `--reference`, without
`=path`.
On success, the command prints the completed pipeline ID, normalized output and
rejected output counts, and the output directory. A debug-enabled run also
prints `debug=<bundle-path>`. If the run completes with warnings, the warning
count is printed to stderr.
Reference flags are resolved against selected chunk, extractor, merger, and
normalizer targets before the run starts. Flat slot names are accepted only
when exactly one selected target declares that slot. For configured reference
bindings, precedence, path resolution, and validation, see
[Configuration](config.md#pipelines).
`--reference` binds or replaces one slot for one selected target. Selectors are:
- `slot=path`: valid when exactly one selected target declares `slot`;
- `chunk.slot=path`: target the chunker;
- `merge.slot=path`: valid when exactly one selected merger declares `slot`;
- `lane.slot=path`: valid when exactly one selected extractor, merger, or
normalizer in that lane declares `slot`;
- `lane.extract.slot=path`: target a lane extractor;
- `lane.merge.slot=path`: target a lane merger;
- `lane.normalize.slot=path`: target a lane normalizer.
Use `slot=path` when the selected targets declare the slot unambiguously:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--reference roster=./campaign-roster.txt
```
Use an explicit selector when multiple selected targets declare the same slot or
when you want to target a specific target:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--reference spells.extract.glossary=./campaign-glossary.txt
```
The same grammar can target chunk, merge, and normalize slots when the configured
modules declare them:
```sh
go run ./cmd/notarius run dnd-session \
--config path/to/config.yml \
--input examples/seriatim-minimal-transcript.json \
--reference chunk.scene_guide=./campaign-scenes.txt \
--reference spells.merge.merge_notes=./merge-notes.txt \
--reference spells.normalize.normalization_notes=./normalization-notes.txt
```
Use `--without-reference` to remove a configured optional binding for a run:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--without-reference glossary
```
Use `--session-id` when an external orchestrator needs all prompt calls from one
run to share an identifier:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--session-id campaign-17-session-04
```
The resume flag can be added to an otherwise identical run invocation. It both
loads compatible checkpoints and records replacements for work executed by that
invocation; without it, the checkpoint root is not used:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--resume
```
Use `--debug` to retain the redacted summary and trace bundle for one run. The
bundle is allocated before pipeline resolution; once allocated, its path is
also printed to stderr if the command fails. Debug-write failures cause exit
code `1`.
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--debug --debug-dir ./notarius-debug
```
Use `refresh` when intentionally replacing the cached plan for the same source:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--chunk_cache refresh
```
Use `bypass` for a one-off run that must not inspect or create plan-cache state:
```sh
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json \
--chunk_cache bypass
```
`--diagnostics-dir` has been removed. For checkpoint behavior, durable output,
debug-bundle lifecycle, and failure inspection, see [Operations](operations.md).
## `config validate`
`notarius config validate` loads and validates configuration.
Flags:
- `--config path`: config file path. If omitted, Notarius uses the discovery
rules in [Configuration](config.md#discovery).
- `--pipeline pipeline-id`: additionally resolve one configured pipeline against
the production module catalog.
- `--only lane-a,lane-b`: validate resolution for selected artifact lanes. This
flag requires `--pipeline`.
Examples:
```sh
go run ./cmd/notarius config validate \
--config examples/dnd-spells.config.yml
go run ./cmd/notarius config validate \
--config examples/dnd-spells.config.yml \
--pipeline dnd-session \
--only spells
```
## `pipelines list`
`notarius pipelines list` prints configured pipeline IDs in sorted order.
Flags:
- `--config path`: config file path. If omitted, Notarius uses the discovery
rules in [Configuration](config.md#discovery).
- `--json`: print `{"pipelines":[...]}` instead of one ID per line.
Examples:
```sh
go run ./cmd/notarius pipelines list \
--config examples/dnd-spells.config.yml
go run ./cmd/notarius pipelines list \
--config examples/dnd-spells.config.yml \
--json
```
## Exit Codes
- `0`: command succeeded.
- `1`: command syntax was valid, but loading config, resolving modules, running
the pipeline, calling the provider, writing output, or writing a requested
debug bundle failed.
- `2`: command syntax was invalid, a command was unknown, a required argument
was missing, or a flag value was malformed.
For YAML structure, defaults, Scriptorium profile sources, environment
overrides, and selectable module and validator keys, see
[Configuration](config.md).