XY-711: Stalled recovery P1: make retained partial progress a first-class outcome

apps/decodex/src/orchestrator/daemon.rs

@@ -434,6 +434,8 @@ where
 			worktree_mapping.as_ref(),
 		)? {
 			Some(ActiveRunDisposition::RetainedReviewComplete)
+		} else if stalled_run_has_retained_partial_progress(worktree_mapping.as_ref()) {
+			Some(ActiveRunDisposition::StalledRetainedPartialProgress { idle_for })
 		} else {
 			Some(ActiveRunDisposition::Stalled { idle_for })
 		}

apps/decodex/src/orchestrator/execution.rs

@@ -420,7 +420,8 @@ fn terminal_failure_lifecycle_event(
 	issue_run: &IssueRunPlan,
 	failure: TerminalFailureLifecycle<'_>,
 ) -> records::LinearExecutionEventRecord {
-	let event_type = if failure.manual_attention_requested {
+	let retained_partial_progress = failure.error_class == "partial_progress_retained";
+	let event_type = if failure.manual_attention_requested || retained_partial_progress {
 		"needs_attention"
 	} else {
 		"terminal_failure"
@@ -447,12 +448,26 @@ fn terminal_failure_lifecycle_event(
 	record.worktree_path = Some(failure.worktree_path.to_owned());
 	record.error_class = Some(failure.error_class.to_owned());
 	record.next_action = Some(failure.next_action.to_owned());
-	record.blockers = Some(vec![format!("Run failed with `{}`.", failure.error_class)]);
-	record.evidence = Some(vec![format!(
-		"Attempt {} reached terminal failure handling.",
-		issue_run.attempt_number
-	)]);
-	record.summary = Some(String::from("Decodex run failed and needs attention."));
+
+	if retained_partial_progress {
+		record.blockers = Some(vec![String::from(
+			"Retained tracked worktree changes require operator recovery.",
+		)]);
+		record.evidence = Some(vec![format!(
+			"Attempt {} stopped with tracked worktree changes retained.",
+			issue_run.attempt_number
+		)]);
+		record.summary = Some(String::from("Decodex retained partial progress and needs attention."));
+		record.terminal_path = Some(String::from("retained_partial_progress"));
+	} else {
+		record.blockers = Some(vec![format!("Run failed with `{}`.", failure.error_class)]);
+		record.evidence = Some(vec![format!(
+			"Attempt {} reached terminal failure handling.",
+			issue_run.attempt_number
+		)]);
+		record.summary = Some(String::from("Decodex run failed and needs attention."));
+	}
+
 	record.pr_url = failure.pr_url.map(ToOwned::to_owned);
 	record.target_state = Some(failure.target_state.to_owned());
 
@@ -1448,6 +1463,7 @@ fn run_failure_requires_terminal_attention(error: &Report) -> bool {
 	error.downcast_ref::<ManualAttentionRequested>().is_some()
 		|| error.downcast_ref::<AppServerZeroEvidenceStartFailure>().is_some()
 		|| error.downcast_ref::<ReviewHandoffNeedsAttention>().is_some()
+		|| error.downcast_ref::<RetainedPartialProgress>().is_some()
 		|| error.downcast_ref::<StalledRunNeedsAttention>().is_some()
 		|| error.downcast_ref::<AppServerCapabilityPreflightFailure>().is_some()
 		|| error.downcast_ref::<AppServerHomePreflightFailure>().is_some()
@@ -1626,6 +1642,7 @@ fn retained_partial_progress_error(
 fn terminal_failure_has_specific_error_class(error: &Report) -> bool {
 	error.downcast_ref::<ManualAttentionRequested>().is_some()
 		|| error.downcast_ref::<ReviewHandoffNeedsAttention>().is_some()
+		|| error.downcast_ref::<RetainedPartialProgress>().is_some()
 		|| error.downcast_ref::<AgentGitCredentialsUnavailable>().is_some()
 		|| error.downcast_ref::<AppServerCapabilityPreflightFailure>().is_some()
 		|| error.downcast_ref::<AppServerHomePreflightFailure>().is_some()

apps/decodex/src/orchestrator/reconciliation.rs

@@ -64,6 +64,8 @@ where
 				worktree_mapping.as_ref(),
 			)? {
 				Some(ActiveRunDisposition::RetainedReviewComplete)
+			} else if stalled_run_has_retained_partial_progress(worktree_mapping.as_ref()) {
+				Some(ActiveRunDisposition::StalledRetainedPartialProgress { idle_for })
 			} else {
 				Some(ActiveRunDisposition::Stalled { idle_for })
 			}
@@ -150,12 +152,17 @@ where
 	else {
 		return Ok(Vec::new());
 	};
+	let disposition = if stalled_run_has_retained_partial_progress(worktree_mapping.as_ref()) {
+		ActiveRunDisposition::StalledRetainedPartialProgress { idle_for }
+	} else {
+		ActiveRunDisposition::Stalled { idle_for }
+	};
 
 	Ok(vec![ActiveRunReconciliation {
 		issue,
 		run_attempt,
 		worktree_mapping,
-		disposition: ActiveRunDisposition::Stalled { idle_for },
+		disposition,
 		workflow: workflow.clone(),
 	}])
 }
@@ -241,6 +248,16 @@ where
 					*idle_for,
 				)?;
 			},
+			ActiveRunDisposition::StalledRetainedPartialProgress { idle_for } => {
+				reconcile_stalled_retained_partial_progress_run(
+					tracker,
+					project,
+					state_store,
+					worktree_manager,
+					&action,
+					*idle_for,
+				)?;
+			},
 			ActiveRunDisposition::StalledAlreadyNeedsAttention { idle_for } => {
 				reconcile_stalled_attention_run(project, state_store, &action, *idle_for)?;
 			},
@@ -361,6 +378,84 @@ where
 	state_store.update_run_status(action.run_attempt.run_id(), "stalled")?;
 	state_store.clear_lease(&action.issue.id)?;
 
+	let issue_run = stalled_reconciliation_issue_run(state_store, worktree_manager, action)?;
+
+	write_reconciliation_operation_marker_best_effort(
+		&issue_run.worktree.path,
+		&issue_run.run_id,
+		issue_run.attempt_number,
+		RUN_OPERATION_RECONCILIATION,
+	);
+	handle_failure(
+		tracker,
+		project,
+		&action.workflow,
+		state_store,
+		&issue_run,
+		&Report::new(StalledRunNeedsAttention {
+			issue_identifier: action.issue.identifier.clone(),
+			run_id: action.run_attempt.run_id().to_owned(),
+			idle_for,
+		}),
+	)?;
+
+	Ok(())
+}
+
+fn reconcile_stalled_retained_partial_progress_run<T>(
+	tracker: &T,
+	project: &ServiceConfig,
+	state_store: &StateStore,
+	worktree_manager: &WorktreeManager,
+	action: &ActiveRunReconciliation,
+	idle_for: Duration,
+) -> Result<()>
+where
+	T: IssueTracker,
+{
+	tracing::warn!(
+		project_id = project.service_id(),
+		issue_id = action.issue.id,
+		issue = action.issue.identifier,
+		run_id = action.run_attempt.run_id(),
+		disposition = "stalled_retained_partial_progress",
+		idle_for_s = idle_for.as_secs(),
+		"Reconciling stalled run with retained partial progress."
+	);
+
+	state_store.update_run_status(action.run_attempt.run_id(), "stalled")?;
+	state_store.clear_lease(&action.issue.id)?;
+
+	let issue_run = stalled_reconciliation_issue_run(state_store, worktree_manager, action)?;
+	let worktree_path = relative_worktree_path(project, &issue_run.worktree);
+
+	write_reconciliation_operation_marker_best_effort(
+		&issue_run.worktree.path,
+		&issue_run.run_id,
+		issue_run.attempt_number,
+		RUN_OPERATION_RECONCILIATION,
+	);
+	handle_failure(
+		tracker,
+		project,
+		&action.workflow,
+		state_store,
+		&issue_run,
+		&Report::new(RetainedPartialProgress {
+			issue_identifier: action.issue.identifier.clone(),
+			run_id: action.run_attempt.run_id().to_owned(),
+			worktree_path,
+		}),
+	)?;
+
+	Ok(())
+}
+
+fn stalled_reconciliation_issue_run(
+	state_store: &StateStore,
+	worktree_manager: &WorktreeManager,
+	action: &ActiveRunReconciliation,
+) -> Result<IssueRunPlan> {
 	let worktree = action.worktree_mapping.as_ref().map_or_else(
 		|| worktree_manager.plan_for_issue(&action.issue.identifier),
 		|mapping| WorktreeSpec {
@@ -372,7 +467,8 @@ where
 	);
 	let retry_budget_base =
 		retry_budget_base_for_issue_worktree(state_store, &action.issue.id, &worktree.path)?;
-	let issue_run = IssueRunPlan {
+
+	Ok(IssueRunPlan {
 		issue: action.issue.clone(),
 		issue_state: planned_issue_state_for_dispatch(
 			&action.workflow,
@@ -388,28 +484,7 @@ where
 		attempt_number: action.run_attempt.attempt_number(),
 		run_id: action.run_attempt.run_id().to_owned(),
 		retry_budget_base,
-	};
-
-	write_reconciliation_operation_marker_best_effort(
-		&issue_run.worktree.path,
-		&issue_run.run_id,
-		issue_run.attempt_number,
-		RUN_OPERATION_RECONCILIATION,
-	);
-	handle_failure(
-		tracker,
-		project,
-		&action.workflow,
-		state_store,
-		&issue_run,
-		&Report::new(StalledRunNeedsAttention {
-			issue_identifier: action.issue.identifier.clone(),
-			run_id: action.run_attempt.run_id().to_owned(),
-			idle_for,
-		}),
-	)?;
-
-	Ok(())
+	})
 }
 
 fn reconcile_stalled_attention_run(
@@ -456,6 +531,15 @@ fn write_reconciliation_operation_marker_best_effort(
 	}
 }
 
+fn stalled_run_has_retained_partial_progress(
+	worktree_mapping: Option<&WorktreeMapping>,
+) -> bool {
+	match worktree_mapping {
+		Some(mapping) => worktree_has_tracked_changes(mapping.worktree_path()),
+		None => false,
+	}
+}
+
 fn retained_review_handoff_matches_run(
 	state_store: &StateStore,
 	run_attempt: &RunAttempt,

apps/decodex/src/orchestrator/run_cycle.rs

@@ -2786,6 +2786,10 @@ where
 	};
 	let disposition = if needs_attention {
 		ActiveRunDisposition::StalledAlreadyNeedsAttention { idle_for }
+	} else if is_issue_active_for_run(issue, context.workflow)
+		&& worktree_has_tracked_changes(worktree_mapping.worktree_path())
+	{
+		ActiveRunDisposition::StalledRetainedPartialProgress { idle_for }
 	} else if is_issue_active_for_run(issue, context.workflow) {
 		ActiveRunDisposition::Stalled { idle_for }
 	} else {

apps/decodex/src/orchestrator/selection.rs

@@ -154,10 +154,22 @@ fn format_terminal_failure_comment(
 	next_action: &str,
 ) -> String {
 	let pr_url_line = pr_url.map_or_else(String::new, |pr_url| format!("\n- pr_url: `{pr_url}`"));
+	let retained_partial_progress = error_class == "partial_progress_retained";
+	let heading = if retained_partial_progress {
+		"decodex retained partial progress and needs attention"
+	} else {
+		"decodex run failed and needs attention"
+	};
+	let timestamp_label = if retained_partial_progress { "recorded_at" } else { "failed_at" };
+	let error_summary = if retained_partial_progress {
+		"Sensitive runtime details were withheld from the tracker comment; inspect the retained lane for the full recovery context."
+	} else {
+		"Sensitive runtime details were withheld from the tracker comment; inspect the local lane for the full failure context."
+	};
 
 	format!(
-		"decodex run failed and needs attention\n\n- run_id: `{run_id}`\n- attempt: `{attempt_number}`\n- failed_at: `{failed_at}`\n- branch: `{branch}`{pr_url_line}\n- worktree_path: `{worktree}`\n- error_class: `{error_class}`\n- next_action: `{next_action}`\n- error_summary: `Sensitive runtime details were withheld from the tracker comment; inspect the local lane for the full failure context.`",
-		failed_at = current_timestamp(),
+		"{heading}\n\n- run_id: `{run_id}`\n- attempt: `{attempt_number}`\n- {timestamp_label}: `{timestamp}`\n- branch: `{branch}`{pr_url_line}\n- worktree_path: `{worktree}`\n- error_class: `{error_class}`\n- next_action: `{next_action}`\n- error_summary: `{error_summary}`",
+		timestamp = current_timestamp(),
 		branch = branch_name,
 		worktree = worktree_path
 	)

apps/decodex/src/orchestrator/tests/operator/status/queue.rs

@@ -813,20 +813,23 @@ fn live_operator_status_snapshot_surfaces_stalled_retained_partial_progress() {
 
 	tracker.issue_comments.borrow_mut().insert(
 		issue.id.clone(),
-		vec![linear_execution_history_comment(
-			&issue,
-			"terminal_failure",
-			"2026-03-13T09:20:00Z",
-			"stalled-retained-partial-progress",
-			|record| {
-				record.error_class = Some(String::from("partial_progress_retained"));
-				record.next_action = Some(String::from(
-					"inspect retained worktree `.worktrees/PUB-110`, finish validation and PR handoff or reset the patch manually",
-				));
-				record.summary = Some(String::from("Decodex run retained partial progress."));
-				record.blockers = Some(vec![String::from(
-					"tracked worktree changes were retained after stalled reconciliation",
-				)]);
+			vec![linear_execution_history_comment(
+				&issue,
+				"needs_attention",
+				"2026-03-13T09:20:00Z",
+				"stalled-retained-partial-progress",
+				|record| {
+					record.error_class = Some(String::from("partial_progress_retained"));
+					record.next_action = Some(String::from(
+						"inspect retained worktree `.worktrees/PUB-110`, finish validation and PR handoff or reset the patch manually",
+					));
+					record.terminal_path = Some(String::from("retained_partial_progress"));
+					record.summary = Some(String::from(
+						"Decodex retained partial progress and needs attention.",
+					));
+					record.blockers = Some(vec![String::from(
+						"tracked worktree changes were retained after stalled reconciliation",
+					)]);
 				record.evidence = Some(vec![String::from(
 					"worktree `.worktrees/PUB-110` has tracked changes",
 				)]);