notarius/docs/operations.md

# Operations

This is the canonical reference for operating implemented Notarius runs.

## Normal Run

A run reads one source file, resolves one configured pipeline, executes its
modules, writes durable output, and writes diagnostics when enabled. Start with
the [README quickstart](../README.md), then use the [CLI reference](cli.md) for
invocation options.

For production, configure an application-owned workspace such as
`/var/lib/notarius` and ensure the Notarius process can create files below it.
For local development, prefer an ignored project-local workspace such as
`./.notarius/workspace`. See [Configuration](config.md#workspace) for workspace
fields.

## Output Directory

Durable output is written to:

```text
<output-root>/<run-id>/
```

The output root and its invocation-specific override are defined in the
[CLI reference](cli.md#run). Output writes are atomic per file. The
[JSON output contract](integrations/json-output.md) defines the logical files,
paths, schemas, and media types inside each run directory.

## Diagnostics Directory

Diagnostics are written under:

```text
<diagnostics-work-dir>/<run-id>/
```

When a workspace directory is configured, diagnostics are written under
`<workspace.directory>/diagnostics/<run-id>/`. An invocation-specific override
changes only the diagnostics root, not the workspace root. Configuration and
environment controls are defined in [Configuration](config.md); the override
flag is defined in the [CLI reference](cli.md#run).

Diagnostics can be disabled through configuration. When disabled, Notarius
does not create a diagnostics run directory or write diagnostics artifacts;
concise failures are still printed to stderr.

Implemented diagnostics artifacts:

- `invocation.json`: command metadata such as operation, config path, input
  path, selected lanes, run ID, and pipeline digest when available.
- `effective-config.json`: resolved config without raw API keys.
- `resolved-pipeline.json`: resolved module bindings and pipeline digest.
- `resolved-references.json`: resolved reference provenance, including target
  stage, lane ID when present, origin, digest, media type, byte size, and
  binding source, without reference content.
- `checkpoint-events.json`: checkpoint steps that were reused or executed
  during an explicit resume invocation.
- `run-manifest.json`: the same run manifest written to durable output when it
  is available, including top-level module metadata when present.
- `warnings.json`: warning list.
- `run-report.json`: counts, status, output path, diagnostics path, and run ID.
- `error.log`: failure message, written after diagnostics directory creation
  when a run fails.

## Checkpoints

When checkpoint writing is enabled for a configured workspace, runs write
checkpoints under:

```text
<workspace.directory>/checkpoints/<pipeline-id>/<input-key>-<source-or-input-digest>/<pipeline-digest>/<identity-digest>/
```

Each workflow step owns its own manifest and payload files. There is no
root-level checkpoint summary. Ordinary invocations execute the pipeline
normally and refresh checkpoints. An explicit resume invocation reuses valid
checkpoints and executes any missing, invalid, or incompatible step normally.
Configuration controls checkpoint writing, while the explicit resume option is
defined in the [Configuration](config.md#workspace) and
[CLI](cli.md#run) references.

Checkpoints do not include raw prompts, raw reference contents, raw LLM request
payloads, or debug traces. They can still contain source text, intermediate
extracted content, rejected outputs, metadata, warnings, and content digests.
Treat checkpoint directories as sensitive local state.

A checkpoint is reused only when its stored status, dependencies, payloads, and
digests match the current invocation. Changes to input bytes, the resolved
pipeline, selected lanes, the runtime LLM profile override, or bound reference
content invalidate reuse. The resolved pipeline identity includes effective
default and explicitly overridden validator chains, so adding, removing,
reordering, or reconfiguring a validator invalidates checkpoints even when the
pipeline profile itself is unchanged.

Typed artifact checkpoints additionally record codec-owned bytes, artifact
kind, schema ID and version, exact schema digest, and media type. A missing or
mismatched codec identity, or bytes the current codec cannot decode, is reported
as a checkpoint reuse miss. The affected operation executes normally and, when
checkpoint writing is enabled, replaces the incompatible checkpoint.

Current checkpoint manifests use workspace schema `notarius.workspace.v2`.
Manifests written with `notarius.workspace.v1` are incompatible because their
chunk provenance has an older shape. On the first explicit resume after an
upgrade, each affected checkpoint is treated as a reuse miss and its workflow
step executes normally. The compatibility check does not migrate or delete the
v1 files; when checkpoint writing is enabled, normal execution refreshes the
affected checkpoint files in the current schema.

Runs do not reuse checkpoints unless explicitly requested. Without reuse, the
workflow executes normally and refreshes checkpoint files when checkpointing is
enabled.

## Debug

When debug recording is enabled for a configured workspace, runs write debug
artifacts under:

```text
<workspace.directory>/debug/<run-id>/
```

Debug output is per invocation. It is independent of checkpointing and is not
used for resume. Enabling debug does not write checkpoints, and enabling resume
checkpointing does not write debug output.

Debug artifacts include inputs and outputs for source, chunk, extract, merge,
normalize, and output work, structured LLM request and response data, validator
requests and results, timing, and retry attempt metadata. LLM calls made inside
a retry or validator attempt
write `prompt-000N.json`, `response-000N.json`, and
`response-content-000N.*` files under that attempt directory and are linked from
the attempt `llm_calls` array. Prompt content is written inline in the prompt
artifact. The response metadata and body use the paired files described above;
the body is pretty-printed JSON when possible and raw text otherwise. Merge and
normalize retries use these stable paths:

```text
merge/<lane-id>/attempt-<NN>.json
merge/<lane-id>/attempt-<NN>/prompt-<NNNN>.json
merge/<lane-id>/attempt-<NN>/response-<NNNN>.json
merge/<lane-id>/attempt-<NN>/response-content-<NNNN>.<ext>

normalize/<lane-id>/attempt-<NN>.json
normalize/<lane-id>/attempt-<NN>/prompt-<NNNN>.json
normalize/<lane-id>/attempt-<NN>/response-<NNNN>.json
normalize/<lane-id>/attempt-<NN>/response-content-<NNNN>.<ext>
```

Checkpoint-reused merge and normalize work retains the stage-level input and
output artifacts but has no retry-attempt artifacts because no module attempt
executed. Debug artifacts may contain source material, reference material,
prompt inputs, model outputs, and other sensitive data. Typed artifact
envelopes include domain-neutral codec identity, redacted metadata and content,
and digests of the stable codec bytes. API keys are not written, and obvious
credential-shaped values and sensitive map keys are redacted, but debug
directories should still be protected as sensitive local state.

## Retention

Diagnostics retention uses the effective mode selected through configuration;
see [Configuration](config.md#diagnostics) for the fields, environment
overrides, precedence, and default.

- `auto`: keep failed runs and successful runs with warnings; remove successful
  warning-free runs.
- `always`: keep every diagnostics run directory.
- `never`: remove successful run directories; failed runs are still retained.

## Failures

Failures before diagnostics directory creation, such as a missing config file or
an unusable diagnostics work directory, are printed to stderr and may not have a
diagnostics run directory.

Failures after diagnostics directory creation are printed to stderr and written
to `error.log`. Depending on where the failure occurred, the directory may also
contain artifacts written before the failure.

If durable output writing fails after the pipeline completes, diagnostics are
retained for inspection.

## Warnings

A successful run with warnings exits with code `0`, prints a warning count to
stderr, and writes warnings to durable output and diagnostics when retained.

The [JSON output contract](integrations/json-output.md) defines durable warning
and validation-status fields.

## Cleanup

It is safe to remove specific old run directories after their output and
diagnostics are no longer needed:

```sh
rm -rf /tmp/notarius/run-1234567890
rm -rf ./notarius-output/run-1234567890
```

Workspace checkpoint and debug directories can also be removed when no longer
needed. Remove exact identity or run directories, for example:

```sh
rm -rf /var/lib/notarius/checkpoints/dnd-session/seriatim-abcdef123456/7890abcd1234/identityabcd1234
rm -rf /var/lib/notarius/debug/run-1234567890
```

Use exact run-directory paths. Avoid broad cleanup commands against parent
directories unless they are part of your own operational policy.

## Operational Limits

Provider retries and timeouts are handled by Scriptorium according to the
selected execution profile. Pipeline module retry settings are defined in
[Configuration](config.md#module-bindings). There is no separate CLI retry
command.

Extract worker concurrency and actual provider-call concurrency are separate
limits. Their configuration, defaults, and validation are defined in
[Configuration](config.md#concurrency). Cancellation stops undispatched extract
work; already started work is allowed to finish or observe cancellation before
the run reports failure.

Notarius writes local files only. Remote storage and archive management are not
part of the implemented CLI.