Document and validate Notarius extraction workflows

docs/internal/manifest.md

@@ -50,13 +50,23 @@ The model admits these stage states:
 
 The application runner marks an executing stage running and then succeeded or
 failed in both manifests, persisting each transition. On success it records
-outputs, logs, generated configuration references, and metadata. A successful
-forced rerun marks only succeeded downstream session-stage records stale.
+outputs, logs, generated configuration references, and metadata. Artifact
+records may include optional contract and external provenance objects; old
+manifests remain compatible when those fields are absent. A successful forced
+rerun marks only succeeded downstream session-stage records stale.
+
+A stage may explicitly return a skipped disposition and stable reason. The
+runner persists that outcome in both manifests, clears older outputs for the
+session-stage record, and continues. This self-skip is distinct from deciding
+not to execute an already-succeeded stage and is reconsidered on later runs.
+Skipped results cannot contain outputs.
 
 When an already-succeeded stage is skipped, the invocation run manifest records
 the `skip` action and reason. The session manifest deliberately retains its
 existing succeeded record because it remains the cross-invocation progress
-authority.
+authority. Stages with a resume validator, currently extraction, may reject an
+otherwise eligible skip when the recorded durable result is obsolete; the
+runner marks it stale and executes it.
 
 Session manifest is the authoritative stage-progress ledger across invocations.
 Run manifest is invocation-scoped audit state.
@@ -64,6 +74,7 @@ Run manifest is invocation-scoped audit state.
 ## Invariants
 
 - stage resume/skip decisions are session-manifest driven.
+- self-skipped stages do not retain stale outputs and are reconsidered.
 - force reruns stale downstream succeeded stages.
 - run manifest does not replace session manifest as progress authority.