Add user documentation for Notarius CLI and config

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# go-application-template
# Notarius
Notarius is a Go CLI for extracting structured artifacts from source material
with explicit, configurable pipeline modules.
The current implementation reads Seriatim minimal transcript JSON, chunks the
source units, extracts D&D spell-cast artifacts with an OpenAI-compatible LLM,
and writes JSON output plus diagnostics for each run.
```sh
NOTARIUS_LLM_DEFAULT_BASE_URL=http://127.0.0.1:8080/v1 \
NOTARIUS_LLM_DEFAULT_MODEL=your-model \
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json
```
If the provider requires authentication, set
`NOTARIUS_LLM_DEFAULT_API_KEY` in the environment before running the command.
Outputs are written under `./notarius-output/<run-id>/` unless `--output-dir`
is provided.
Useful references:
- [CLI reference](docs/cli.md)
- [Configuration reference](docs/config.md)
- [Seriatim input contract](docs/integrations/seriatim.md)
- [Maintained example config](examples/dnd-spells.config.yml)
- [Maintained example input](examples/seriatim-minimal-transcript.json)

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# CLI Reference
This is the canonical reference for the implemented Notarius command-line
interface.
## Quick Run
```sh
NOTARIUS_LLM_DEFAULT_BASE_URL=http://127.0.0.1:8080/v1 \
NOTARIUS_LLM_DEFAULT_MODEL=your-model \
go run ./cmd/notarius run dnd-session \
--config examples/dnd-spells.config.yml \
--input examples/seriatim-minimal-transcript.json
```
Set `NOTARIUS_LLM_DEFAULT_API_KEY` if the OpenAI-compatible provider requires
a bearer token.
## Commands
```text
notarius help
notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b]
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 checks
`NOTARIUS_CONFIG`, then `/usr/local/etc/notarius/config.yml`.
- `--only lane-a,lane-b`: run only the named artifact lanes. Values are
comma-separated and must be non-empty.
- `--output-dir path`: output root. The run writes to `<path>/<run-id>/`.
Defaults to `./notarius-output`.
- `--diagnostics-dir path`: diagnostics work directory override for this
invocation.
- `--llm-profile id`: override every effective module binding to use one LLM
profile.
On success, the command prints the completed pipeline ID, approved and rejected
artifact counts, and the output directory. If the run completes with warnings,
the warning count is printed to stderr.
The current `run` command requires the resolved pipeline to use exactly one
distinct LLM profile after defaults and overrides are applied.
## `config validate`
`notarius config validate` loads and validates configuration.
Flags:
- `--config path`: config file path. If omitted, discovery uses
`NOTARIUS_CONFIG`, then `/usr/local/etc/notarius/config.yml`.
- `--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, discovery uses
`NOTARIUS_CONFIG`, then `/usr/local/etc/notarius/config.yml`.
- `--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 diagnostics
failed.
- `2`: command syntax was invalid, a command was unknown, a required argument
was missing, or a flag value was malformed.
## Implemented Production Pipeline Modules
The production CLI currently registers these module keys:
- input: `seriatim`
- chunk: `generic`
- extract: `dnd/spells`
- merge: `appendorder`
- normalize: `noop`
- output: `json`
The production CLI does not currently register validator modules.
For YAML structure, defaults, environment overrides, and module binding syntax,
see [Configuration](config.md).

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# Configuration
This is the canonical reference for implemented Notarius configuration.
Notarius reads YAML config files with `version: 1`. File config is applied over
built-in defaults, then environment overrides are applied.
## Discovery
Commands that accept `--config` load configuration in this order:
1. the `--config` path, when provided;
2. `NOTARIUS_CONFIG`, when set to a non-empty path;
3. `/usr/local/etc/notarius/config.yml`.
If none is available, the command fails with a config file not found error.
## Minimal Example
```yaml
version: 1
llm_profiles:
default:
provider: openai-compatible
base_url: http://127.0.0.1:8080/v1
model: your-model
pipelines:
dnd-session:
input: seriatim
chunk:
module: generic
options:
max_units: 50
artifacts:
spells:
extract: dnd/spells
```
The maintained fixture is [examples/dnd-spells.config.yml](../examples/dnd-spells.config.yml).
## Top-Level Fields
- `version`: required. The only supported value is `1`.
- `llm_profiles`: optional map of LLM profile IDs to profile settings.
- `pipelines`: optional map of pipeline IDs to pipeline definitions.
- `concurrency`: optional global concurrency settings.
- `diagnostics`: optional diagnostics settings.
Unknown YAML fields are rejected.
## Defaults
Built-in defaults:
```yaml
llm_profiles:
default:
provider: openai-compatible
timeout: 600
max_retries: 3
max_concurrency: 1
concurrency:
total_llm: 1
diagnostics:
work_dir: /tmp/notarius
retention: auto
```
No pipelines are built in. A run requires a configured pipeline.
## LLM Profiles
Each `llm_profiles` entry may contain:
- `provider`: optional provider key. Empty means `openai-compatible`; any other
non-empty value must be `openai-compatible`.
- `base_url`: provider base URL. Required for actual LLM calls.
- `model`: provider model name. Required for actual LLM calls.
- `api_key_env`: environment variable name to read for the API key.
- `timeout`: request timeout as whole seconds or a Go-style duration string such
as `10m`.
- `max_retries`: retry count for provider calls. Must be zero or greater.
- `max_concurrency`: per-profile LLM concurrency. Must be zero or greater; when
zero, Notarius uses `concurrency.total_llm`.
Raw API keys are not accepted as file config fields. Use `api_key_env` or an
environment override.
## Environment Overrides
These environment variables are applied after the config file:
- `NOTARIUS_CONFIG`: config discovery path.
- `NOTARIUS_LLM_DEFAULT_API_KEY`: API key for the `default` LLM profile.
- `NOTARIUS_LLM_DEFAULT_BASE_URL`: base URL for the `default` LLM profile.
- `NOTARIUS_LLM_DEFAULT_MODEL`: model for the `default` LLM profile.
- `NOTARIUS_LLM_DEFAULT_TIMEOUT_SECONDS`: integer timeout seconds for the
`default` LLM profile.
- `NOTARIUS_LLM_DEFAULT_MAX_RETRIES`: integer retry count for the `default` LLM
profile.
- `NOTARIUS_LLM_DEFAULT_MAX_CONCURRENCY`: integer max concurrency for the
`default` LLM profile.
- `NOTARIUS_TOTAL_LLM_CONCURRENCY`: integer global LLM concurrency.
- `NOTARIUS_WORK_DIR`: diagnostics work directory.
- `NOTARIUS_DIAGNOSTICS_RETENTION`: diagnostics retention mode.
Integer environment values must parse as base-10 integers.
## Pipelines
A pipeline defines the fixed Notarius workflow:
```text
input -> chunk -> extract -> merge -> normalize -> output
```
Pipeline fields:
- `input`: required module binding.
- `chunk`: optional module binding. Default module is `generic`.
- `artifacts`: required for pipeline resolution. It maps artifact lane IDs to
lane definitions.
- `output`: optional module binding. Default module is `json`.
Artifact lane fields:
- `extract`: required module binding.
- `merge`: optional module binding. Default module is `appendorder`.
- `normalize`: optional module binding. Default module is `noop`.
- `validators`: optional list of module bindings. The production CLI currently
does not register validator modules.
`notarius run` and `notarius config validate --pipeline` resolve the pipeline
against the production module catalog and fail fast for unknown or incompatible
module keys.
## Module Bindings
Every module binding may use shorthand:
```yaml
input: seriatim
```
or object form:
```yaml
chunk:
module: generic
llm_profile: default
options:
max_units: 50
```
Binding fields:
- `module`: module key.
- `llm_profile`: optional LLM profile ID. Empty means `default`.
- `options`: optional module-specific settings.
The `--llm-profile` run flag overrides every effective module binding to use
one configured profile.
## Implemented Production Modules
| Slot | Key | Notes |
| --- | --- | --- |
| input | `seriatim` | Reads Seriatim minimal transcript JSON. |
| chunk | `generic` | Splits source units into ordered chunks. |
| extract | `dnd/spells` | Extracts `dnd.spell_cast` artifacts. |
| merge | `appendorder` | Keeps candidates in append order. |
| normalize | `noop` | Passes merged artifacts through unchanged. |
| output | `json` | Produces JSON output files. |
The `generic` chunker accepts:
- `max_units`: positive integer, default `50`;
- `overlap_units`: non-negative integer, default `0`, and must be less than
`max_units`.
## Diagnostics
`diagnostics` fields:
- `work_dir`: directory for per-run diagnostics. Default: `/tmp/notarius`.
- `retention`: `auto`, `always`, or `never`. Empty uses `auto`.
`auto` retains diagnostics for failed runs and successful runs with warnings.
`always` retains diagnostics for every run. `never` removes diagnostics for
successful runs without regard to warnings; failed runs are retained.
The `--diagnostics-dir` run flag overrides `diagnostics.work_dir` for that
invocation.
## Validation
Configuration validation checks:
- supported config version and known YAML fields;
- non-empty, non-duplicated IDs after trimming;
- supported LLM provider and non-negative profile limits;
- positive global LLM concurrency;
- supported diagnostics retention and non-empty work directory;
- module binding LLM profiles refer to configured profiles.
Pipeline resolution additionally checks:
- the pipeline ID exists;
- at least one artifact lane is declared and selected;
- selected lanes exist when `--only` is used;
- required module keys are present;
- module keys are registered for the expected slot;
- module capability requirements are satisfied.