fix: delete marked worktrees before classification

Author: chubes4

inc/Cli/Commands/WorkspaceCommand.php

@@ -2850,6 +2850,23 @@ private function run_worktree_abandoned_orchestration( array $assoc_args ): arra
 			'source' => self::CLEANUP_CLI_SOURCE,
 		);
 
+		if ( $apply ) {
+			$bounded = $this->run_worktree_abandoned_bounded_apply($abilities['bounded_apply'], $result, true, $force, $limit, 'initial');
+			if ( is_wp_error($bounded) ) {
+				return $bounded;
+			}
+
+			if ( 'bounded' === $stage ) {
+				$prune = $abilities['prune']->execute(array());
+				if ( is_wp_error($prune) ) {
+					return $prune;
+				}
+				$result['steps']['prune'] = $this->summarize_worktree_abandoned_step($prune);
+
+				return $this->finalize_worktree_abandoned_result($result, $apply, $force, $limit, $passes, $until_budget, $started_at);
+			}
+		}
+
 		if ( $stage_order[ $stage ] <= $stage_order['reconcile'] ) {
 			$reconcile_input = array_merge(
 				$common_page,

tests/smoke-worktree-cleanup-cli.php

@@ -1130,6 +1130,7 @@ public function execute( array $input ): array
     datamachine_code_cleanup_assert(JSON_ERROR_NONE === json_last_error(), 'abandoned JSON output parses cleanly');
     datamachine_code_cleanup_assert(true === ( $abandoned_json['applied'] ?? null ), 'abandoned apply mode is explicit in JSON');
     datamachine_code_cleanup_assert(true === ( $abandoned_json['force'] ?? null ), 'abandoned force mode is explicit in JSON');
+    datamachine_code_cleanup_assert('bounded_apply_initial' === array_key_first($abandoned_json['steps'] ?? array()), 'abandoned apply drains already-marked rows before slow classifiers');
     datamachine_code_cleanup_assert(1 === (int) ( $reconcile_metadata_ability->last_input['limit'] ?? 0 ), 'abandoned forwards limit to metadata reconciliation');
     datamachine_code_cleanup_assert(false === ( $reconcile_metadata_ability->last_input['dry_run'] ?? null ), 'abandoned --apply applies metadata reconciliation');
     datamachine_code_cleanup_assert(array( 0, 1 ) === array_map(fn( $input ) => (int) ( $input['offset'] ?? 0 ), array_slice($reconcile_metadata_ability->inputs, -2)), 'abandoned drains metadata reconciliation pages in apply mode');
@@ -1140,7 +1141,7 @@ public function execute( array $input ): array
     datamachine_code_cleanup_assert(true === ( $bounded_apply_ability->last_input['force'] ?? null ), 'abandoned forwards force only to bounded cleanup removal');
     datamachine_code_cleanup_assert(false === ( $bounded_apply_ability->last_input['dry_run'] ?? null ), 'abandoned --apply removes eligible rows');
     datamachine_code_cleanup_assert(1 === $prune_ability->calls, 'abandoned prunes stale git metadata after cleanup pass');
-    datamachine_code_cleanup_assert(1 === (int) ( $abandoned_json['summary']['removed'] ?? 0 ), 'abandoned summary reports removed rows');
+    datamachine_code_cleanup_assert(2 === (int) ( $abandoned_json['summary']['removed'] ?? 0 ), 'abandoned summary reports removed rows from initial and post-classifier drains');
     datamachine_code_cleanup_assert(2 === (int) ( $abandoned_json['summary']['blocked'] ?? 0 ), 'abandoned summary reports blocked rows');
     datamachine_code_cleanup_assert(1 === (int) ( $abandoned_json['summary']['blocked_by_reason']['unpushed_commits'] ?? 0 ), 'abandoned preserves unpushed-commit blocker evidence');
 
@@ -1172,9 +1173,10 @@ public function execute( array $input ): array
     datamachine_code_cleanup_assert(JSON_ERROR_NONE === json_last_error(), 'abandoned stalled remote-clean JSON output parses cleanly');
     datamachine_code_cleanup_assert('remote-clean' === ( $abandoned_remote_clean_stalled_json['continuation']['stage'] ?? '' ), 'abandoned stalled remote-clean emits remote-clean continuation');
     datamachine_code_cleanup_assert(42 === (int) ( $abandoned_remote_clean_stalled_json['continuation']['offset'] ?? -1 ), 'abandoned stalled remote-clean keeps current offset continuation');
-    datamachine_code_cleanup_assert(count($bounded_apply_ability->inputs) === $bounded_call_count_before_stalled_classifier + 1, 'abandoned drains bounded cleanup before returning stalled classifier continuation');
+    datamachine_code_cleanup_assert(count($bounded_apply_ability->inputs) === $bounded_call_count_before_stalled_classifier + 2, 'abandoned drains bounded cleanup before and after stalled classifier continuation');
+    datamachine_code_cleanup_assert('bounded_apply_initial' === array_key_first($abandoned_remote_clean_stalled_json['steps'] ?? array()), 'abandoned stalled classifier run starts with bounded cleanup');
     datamachine_code_cleanup_assert(isset($abandoned_remote_clean_stalled_json['steps']['bounded_apply_remote-clean']), 'abandoned stalled classifier output includes bounded cleanup step');
-    datamachine_code_cleanup_assert(1 === (int) ( $abandoned_remote_clean_stalled_json['summary']['removed'] ?? 0 ), 'abandoned stalled classifier summary includes bounded removals');
+    datamachine_code_cleanup_assert(2 === (int) ( $abandoned_remote_clean_stalled_json['summary']['removed'] ?? 0 ), 'abandoned stalled classifier summary includes bounded removals');
     $active_remote_clean_ability->stall_at_offset = null;
 
     $reconcile_metadata_ability->stall_at_offset = 90;