# Operations This is the canonical reference for operating implemented Notarius runs. ## Normal Run A run reads one source file, resolves one configured pipeline, calls the configured Scriptorium-backed LLM runtime, writes durable JSON output, and writes diagnostics for inspection. ```sh go run ./cmd/notarius run dnd-session \ --config examples/dnd-spells.config.yml \ --input examples/seriatim-minimal-transcript.json \ --output-dir ./notarius-output \ --diagnostics-dir /tmp/notarius ``` The command prints a success line with the pipeline ID, normalized output count, rejected output count, and the output path. ## Output Directory Durable output is written to: ```text // ``` The default output root is `./notarius-output`. Use `--output-dir` to choose a different root. The `json` output module writes these files: - `index.json`: file index with paths to the manifest, lane output files, rejected outputs, and warnings. - `manifest.json`: run manifest with resolved pipeline provenance, top-level module metadata, module keys, reference provenance, validation status, and timing. - `lanes/.json`: normalized raw JSON output payloads, one file per lane. For the current D&D spell extractor, this includes `lanes/spells.json`. - `rejected.json`: rejected raw output records. - `warnings.json`: warnings reported by pipeline modules or the output encoder. Output writes are atomic per file. Logical output file names must be clean, relative, slash-separated paths and must not contain `..`. ## Diagnostics Directory Diagnostics are written under: ```text // ``` The default diagnostics work directory is `/tmp/notarius`. It can be set with `workspace.directory`, `NOTARIUS_WORKSPACE_DIR`, legacy `diagnostics.work_dir`, legacy `NOTARIUS_WORK_DIR`, or `--diagnostics-dir`. When a workspace directory is set, diagnostics are written under `/diagnostics//` unless `--diagnostics-dir` overrides the diagnostics work directory for that invocation. Set `workspace.diagnostics.enabled: false` or `NOTARIUS_WORKSPACE_DIAGNOSTICS_ENABLED=false` to skip diagnostics directory creation and diagnostics artifact writes. 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. `source-document.json` is supported by the diagnostics writer but is not written by the current CLI run workflow. ## Checkpoints When `workspace.resume.enabled: true` and `workspace.directory` is set, runs write checkpoints under: ```text /checkpoints//-// ``` Each workflow step owns its own manifest and payload files. There is no root-level checkpoint summary. Ordinary `notarius run` invocations execute the pipeline normally and refresh checkpoints. `notarius run --resume` reuses valid checkpoints and executes any missing, invalid, or incompatible step normally. Checkpoint payloads preserve byte content with base64 envelopes, media type, metadata, warnings, and content digests where applicable. Checkpoints do not include raw prompts, raw reference contents, raw LLM request payloads, or debug traces. A checkpoint is reused only when its workspace schema version, checkpoint identity digest, step status, dependency fingerprints, payload files, and payload digests match the current invocation. Changes to input bytes, resolved pipeline digest, selected lanes, runtime LLM profile override, or materialized reference digests invalidate reuse. ## Debug When `workspace.debug.enabled: true` and `workspace.directory` is set, runs write debug artifacts under: ```text /debug// ``` 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 framework-boundary inputs and outputs for source, chunk, extract, merge, normalize, and output work, structured LLM request and response data from Notarius contracts, validator requests and results, timing, and retry attempt metadata. Debug artifacts may contain source material, reference material, prompt inputs, model outputs, and other sensitive data. Obvious credential-shaped values and sensitive map keys are redacted, but debug directories should still be protected as sensitive local state. ## Retention Diagnostics retention is configured with `workspace.diagnostics.retention`, `NOTARIUS_WORKSPACE_DIAGNOSTICS_RETENTION`, legacy `diagnostics.retention`, legacy `NOTARIUS_DIAGNOSTICS_RETENTION`, or the default `auto`. - `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. Unknown retention values are rejected during config validation. ## 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, diagnostics may also include invocation metadata, redacted effective config, resolved pipeline data, the run manifest, warnings, and a run report. If durable output writing fails after the pipeline completes, diagnostics are retained for inspection and may include `run-manifest.json`, `warnings.json`, `run-report.json`, and `error.log`. ## 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 run manifest `validation_status` indicates whether raw outputs were approved or rejected after validation. Reference-related warnings include empty bound reference files. Empty references are still passed to extractors so optional slots can be intentionally blank. ## 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 ``` Use exact run-directory paths. Avoid broad cleanup commands against parent directories unless they are part of your own operational policy. ## Operational Limits If `--resume` cannot reuse a checkpoint, Notarius executes that step and writes a fresh checkpoint when checkpointing is enabled. Provider retries and timeouts are handled by Scriptorium according to the selected execution profile. Pipeline module retries are controlled by module binding `retries` values in config for chunk, extract, merge, and normalize. There is no separate CLI retry command. Notarius writes local files only. Remote storage and archive management are not part of the implemented CLI.