notarius/docs/operations.md

Operations

This is the canonical guide to operating Notarius filesystem state. Command syntax is in the CLI reference; field definitions and precedence are in Configuration.

State Model

Notarius uses three independent filesystem surfaces:

• output is durable user data;
• cache is reconstructible chunk-plan and checkpoint state; and
• debug is explicitly requested inspection data.

Choose separate roots and access controls for each surface. A normal run writes durable output, may use the chunk-plan cache, and records checkpoints when cache.checkpoints.enabled is true. It does not create debug state unless its invocation includes --debug.

Output

Durable logical files are written under:

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

The CLI generates one run ID in the form run-<started-at-unix-nanoseconds>-<32-lowercase-hex-characters> and uses it for output, manifests, and any requested debug bundle. It validates every logical output name before exclusively creating the run directory. If that directory already exists, the invocation fails without changing it.

Each output file is written atomically. A later file-write failure leaves the newly allocated partial run directory in place for inspection; Notarius never automatically removes output. The JSON output contract owns the logical file names, schemas, and media types inside a run directory.

Remove an output run directory only after its consumer data is no longer needed. This is data deletion, not cache cleanup.

Ordered D&D Workflow

The maintained NPC-grounded configuration contains one pipeline with two ordered steps. The first step extracts and normalizes NPCs. Only after that lane reaches an accepted terminal result does the second step begin; its generated NPC reference is supplied in memory to spell extraction, combat extraction, and combat normalization.

go run ./cmd/notarius run dnd-npc-grounded \
  --config examples/dnd-npc-grounded.config.yml \
  --input examples/seriatim-minimal-transcript.json \
  --output-dir ./npc-grounded-output

The NPC artifact grounds canonical names through a names-only prompt projection, not spell or combat evidence. Current-transcript source ranges remain the only event evidence. The manifest records generated-reference identity and bounded producer provenance; it does not record generated payload content, and no generated content is exposed through a filesystem path. The same producer artifact may fan out to compatible consumers, while a missing or rejected producer prevents the later step from starting.

Standalone module configurations continue to support external NPC files when a workflow intentionally crosses a process or session boundary. Those files are validated against the consumer slot and must be protected as sensitive campaign data. They are not part of the maintained ordered handoff workflow.

Chunk-Plan Cache

Chunk plans are stored at:

<chunk-plan-root>/<source-sha256-hex>/plan.json

auto reuses a complete valid plan or regenerates missing or invalid state. refresh regenerates and atomically replaces a plan after chunk validation. bypass performs no plan-cache I/O and does not resolve or create the root. Plan selection is source-addressed and independent of checkpoint and debug roots.

When its directory is empty in configuration, the root is <os.UserCacheDir>/notarius/chunk-plans. A configured directory is the exact root; no suffix is appended. Directories and files created by the store use 0700 and 0600 permissions on supported Unix systems. The configured root is a trust boundary: do not share it among mutually untrusted users.

Remove an exact digest directory or the configured root only when accepting the cost of recomputing plans and any chunk-stage work. Cache publication is atomic; there is no history, locking, garbage collection, or rollback facility.

For a Linux service account, provision a dedicated restrictive root such as:

cache:
  chunk_plans:
    directory: /var/cache/notarius/chunk-plans

Checkpoint Cache

Checkpoint recording is controlled by cache.checkpoints.enabled, which defaults to false. When enabled, every run records running, succeeded, and failed transitions and reusable validator-approved results. Successful, rejected, and failed runs may therefore all leave checkpoint state. The --resume flag additionally loads compatible completed work before executing missing or incompatible stages. Without --resume, a recording-enabled run never loads checkpoints. Using --resume while recording is disabled is an error.

Checkpoints use the selected root and the existing identity hierarchy:

<checkpoint-root>/<pipeline-id>/<input-key>-<source-or-input-digest>/<pipeline-digest>/<identity-digest>/...

The final identity digest includes stable semantic fingerprints explicitly contributed by prepared modules and validators. Adding or changing one of these fingerprints intentionally causes a cold cache miss; old checkpoint directories are left in place and are never migrated or deleted automatically.

An empty configured directory selects <os.UserCacheDir>/notarius/checkpoints. The root is exact when configured. Created directories and files use 0700 and 0600 permissions on supported Unix systems.

Checkpoint payloads can contain source text, intermediate artifacts, metadata, warnings, and content digests. Treat them as sensitive derived application data. Compatible files from a former checkpoint root remain reusable when cache.checkpoints.directory names that exact existing root. They are not moved, migrated, or deleted automatically. The frozen serialized identifier workspace_schema_version remains part of checkpoint compatibility; it is not a configuration setting.

For a Linux service account, independently provision:

cache:
  checkpoints:
    enabled: true
    directory: /var/cache/notarius/checkpoints

Remove an exact checkpoint identity directory or the configured root only when recomputation is acceptable.

Resume And Selective Recompute

--resume loads compatible accepted work only when checkpoint recording is enabled. A normal resumed run may reuse source, extract, merge, and normalize checkpoints independently and may recompute a stage after a cache miss. Generated references add a dependency fingerprint for the producer's artifact kind, schema identity, media type, canonical content digest, and size. If that fingerprint changes or the producer is missing, dependent checkpoints are invalidated; unrelated work remains eligible for reuse.

--recompute-step <step-id> requires both --resume and cache.checkpoints.enabled: true. It forces the named step and all transitive dependents to execute, while compatible predecessors and unrelated lanes remain reusable. The ID may be an explicit configured step or default for an implicit single-step pipeline. It cannot be combined with --only, and it does not change the persistent identity of otherwise identical checkpoints. Decisions are bounded and categorized as reused, executed, forced_recompute, or dependency_invalidated.

For an unselected producer required by a recomputed step, Notarius loads the accepted normalized artifact directly. Valid normalize state is sufficient even when that producer's extract or merge checkpoint is missing or corrupt. The normalize manifest must be successful and match workspace schema v3, the exact current invocation identity, step, lane, and normalizer; its payload digest and canonical codec representation must also validate. A forced producer bypasses this lookup and executes.

If a required predecessor's accepted normalized artifact is missing, rejected, corrupt, non-canonical, or incompatible, the run fails before the dependent step starts. It does not fall back to rerunning that predecessor. The failure manifest retains completed upstream outcomes and dependency context but not generated reference content. For diagnosis, first check the producer step and lane in the manifest, then inspect checkpoint decision categories and reason codes. Rerun the producer explicitly rather than copying an artifact into the checkpoint root.

The decision that caused a required-predecessor failure is retained before the run returns, and the CLI error identifies its step, lane, and reason code.

Checkpoint reason codes are stable diagnostic identifiers:

Reason code	Operator meaning
loading_disabled	This invocation did not enable checkpoint loading.
checkpoint_missing	The requested checkpoint file does not exist.
checkpoint_path_invalid	The requested checkpoint location failed confinement validation.
checkpoint_read_failed	An existing checkpoint could not be read.
checkpoint_decode_failed	Checkpoint JSON could not be decoded.
workspace_schema_incompatible	The stored workspace schema is not supported by this build.
identity_mismatch	The stored invocation identity differs from the current invocation.
stage_mismatch, step_mismatch, lane_mismatch, module_mismatch	Stored scope does not match the requested pipeline scope.
status_not_reusable	The stored operation did not finish in a reusable status.
dependency_mismatch	Stored dependencies differ; the category is dependency_invalidated.
artifact_payload_invalid	Stored artifact payload structure or encoding is invalid.
artifact_digest_mismatch	Stored artifact bytes do not match their recorded digest.
artifact_codec_incompatible	Stored artifact identity is incomplete or incompatible with the codec contract.
artifact_not_canonical	The codec can decode the artifact, but its bytes are not canonical.
checkpoint_reused	The stored checkpoint passed validation and was reused.
accepted_artifact_reused	A required producer's accepted normalized artifact was canonically validated and hydrated.
recompute_step	Selective recomputation forced execution of this lane.

Decision detail is bounded explanatory text derived from the stable reason code, not caller-supplied prose or a data-recovery channel. It never contains checkpoint paths, artifact or reference content, source content, credentials, or environment values.

Debug Bundles

Only notarius run --debug enables debug collection. The selected root contains one retained bundle per invocation:

<debug-root>/<run-id>/
  summary/
  trace/

summary/ contains redacted invocation, effective-configuration, resolved pipeline and reference provenance, checkpoint and chunk-plan decisions, run manifest, warnings, report, and any available error text. It excludes raw source, references, annotations, prompts, model responses, credentials, and malformed cache bytes.

trace/ contains application-owned execution detail, including source and stage material, plans, chunks, validator attempts, prompts, model responses, timing, and serialized artifacts. It may retain application data omitted from output. Credentials, credential-shaped values, sensitive metadata, unrelated environment values, and unrelated filesystem content are not captured.

Bundles inherit the sensitivity of the application data they capture. Their additional risk comes from copying and aggregating that data, so restrict access, avoid shared roots between untrusted users, and define retention outside Notarius. Created bundle directories use 0700 and files use 0600 on supported Unix systems.

Notarius never automatically deletes a requested bundle. If allocation succeeds, its path is reported on success and failure. A requested summary or trace write failure makes the command fail, preserving whatever bundle data was already written for inspection. Every allocated bundle makes one best-effort attempt to record a terminal run-report.json.

Failures And Warnings

Failures before debug allocation are reported on stderr without a bundle. Failures after allocation report the bundle path on stderr and make independent attempts to write a failure run-report.json and error.log. The report retains the paths and pipeline outcome fields known at the failure point. If either terminal write fails, the original command error remains first on stderr, followed by the persistence error and bundle path. An output-write failure leaves the allocated bundle in place. A successful run with warnings exits 0, reports a warning count on stderr, and records warnings in durable output and any requested debug summary.

Cleanup

Use exact paths for manual cleanup. Examples:

rm -rf ./notarius-output/run-1721300000000000000-0123456789abcdef0123456789abcdef
rm -rf /var/cache/notarius/chunk-plans/0123abcd
rm -rf /var/cache/notarius/checkpoints/pipeline/input-0123/pipeline-4567/identity-89ab
rm -rf ./notarius-debug/run-1721300000000000000-0123456789abcdef0123456789abcdef

Avoid broad recursive cleanup against a parent root unless it is an explicit operator policy. Output deletion is permanent user-data loss. Cache deletion is recoverable but can repeat expensive work. Debug deletion removes troubleshooting evidence and any retained application-data copy.

Operational Limits

Provider retries and timeouts are handled by Scriptorium according to the selected execution profile. Pipeline module retry settings are defined in Configuration. Extract worker concurrency and actual provider-call concurrency are separate limits; their fields and validation are defined in Configuration. Notarius writes local files only; remote storage and archive management are outside the implemented CLI.