Close analyze checkpointing documentation

docs/internal/stage-analyze.md

@@ -31,12 +31,14 @@ Supported source families:
 ## Key Behavior
 
 - when `pipeline.scriptorium` is absent or no configured artifact is
-  executable, completes successfully with no outputs and records explanatory
-  metadata. This is not an explicit self-skip: the session manifest records success,
-  satisfy publish's prerequisite, and an ordinary later run reuses the result
-  while the effective set remains empty. Enabling or selecting an artifact
-  later makes missing versioned evidence non-resumable and schedules it without
-  requiring force.
+  executable, completes successfully and records explanatory metadata. Before
+  returning, it reconciles and checkpoints the complete session collection:
+  records removed from configuration are dropped, while valid records for
+  configured but unselected artifacts remain authoritative. This is not an
+  explicit self-skip: the session manifest records success, satisfies publish's
+  prerequisite, and an ordinary later run reuses the result while the effective
+  set remains empty. Enabling or selecting an artifact later makes missing
+  versioned evidence non-resumable and schedules it without requiring force.
 - builds a runtime artifact catalog containing built-ins, configured artifacts,
   and configured extraction lanes. Extraction availability is hydrated only
   from compatible successful extraction evidence.
@@ -95,7 +97,8 @@ Supported source families:
 - implements aggregate resume validation by running the same read-only catalog,
   fingerprint reconciliation, and work planner used by execution. A succeeded
   aggregate record is reusable exactly when the selected closure schedules no
-  artifact work; stale unrelated records do not block a partial selection.
+  artifact work and no removed configuration records require a checkpoint;
+  stale unrelated records do not block a partial selection.
 - exposes the typed artifact decision to `session plan`. Planning applies it to
   a cloned manifest after modeling earlier selected stage transitions, so
   aggregate run/skip and artifact execute/reuse decisions match the ordinary
@@ -184,13 +187,18 @@ Supported source families:
 - [CLI](../cli.md) owns user-visible artifact selection.
 - [Scriptorium](../integrations/scriptorium.md) owns the subprocess contract.
 - Implementation and tests: `internal/stage/analyze.go`,
-  `internal/stage/analyze_input_identity.go`, `internal/stage/analyze_test.go`,
-  `internal/stage/analyze_input_identity_test.go`,
+  `internal/stage/analyze_artifact_execution.go`,
+  `internal/stage/analyze_execution_state.go`,
+  `internal/stage/analyze_input_identity.go`,
   `internal/stage/analyze_fingerprint.go`,
+  `internal/stage/analyze_reconciliation.go`, `internal/stage/analyze_plan.go`,
+  `internal/stage/analyze_resume.go`, `internal/stage/analyze_test.go`,
+  `internal/stage/analyze_checkpoint_test.go`,
+  `internal/stage/analyze_input_identity_test.go`,
   `internal/stage/analyze_fingerprint_test.go`,
-  `internal/stage/analyze_reconciliation.go`, and
   `internal/stage/analyze_reconciliation_test.go`,
-  `internal/stage/analyze_plan.go`, `internal/stage/analyze_plan_test.go`, and
-  `internal/stage/analyze_incremental_execution_test.go`, and
+  `internal/stage/analyze_plan_test.go`,
+  `internal/stage/analyze_incremental_execution_test.go`,
   `internal/stage/analyze_failure_test.go`,
-  `internal/stage/analyze_resume.go`, and `internal/stage/analyze_resume_test.go`
+  `internal/stage/analyze_resume_test.go`, and
+  `internal/app/analyze_checkpoint_recovery_test.go`.