Write workspace checkpoints during runs

docs/operations.md

@@ -84,6 +84,24 @@ Implemented diagnostics artifacts:
 `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
+<workspace.directory>/checkpoints/<pipeline-id>/<input-key>-<source-digest>/<pipeline-digest>/
+```
+
+Each workflow step owns its own manifest and payload files. There is no
+root-level checkpoint summary. Current runs write checkpoints for inspection and
+future recovery support only; the CLI does not read checkpoints or skip work.
+
+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.
+
 ## Retention
 
 Diagnostics retention is configured with `workspace.diagnostics.retention`,
@@ -138,8 +156,8 @@ directories unless they are part of your own operational policy.
 
 ## Operational Limits
 
-There is no command to resume a failed run. Re-run `notarius run` after fixing
-the cause.
+Checkpoint writing does not provide resume execution yet. Re-run `notarius run`
+after fixing the cause of a failed run.
 
 Provider retries and timeouts are handled by Scriptorium according to the
 selected execution profile. Pipeline module retries are controlled by module