Fix bounded cleanup run apply batches

[chubes4]

Summary

• Bounds DB-backed cleanup apply / resume to a small row batch instead of applying every pending artifact and worktree row synchronously.
• Marks partially applied runs as needs_resume with a concrete resume command instead of leaving long-running operator sessions silent or stuck in applying.
• Wires --limit through CLI and ability inputs, and adds smoke coverage for bounded apply/resume sequencing.

Fixes #550.

Verification

• php -l inc/Workspace/CleanupRunService.php && php -l inc/Abilities/WorkspaceAbilities.php && php -l inc/Cli/Commands/WorkspaceCommand.php && php -l tests/smoke-cleanup-run-storage.php && php -l tests/smoke-worktree-cleanup-cli.php
• php tests/smoke-cleanup-run-storage.php
• php tests/smoke-worktree-cleanup-cli.php
• git diff --check

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (GPT-5.5)
• Used for: Diagnosing the cleanup apply timeout, implementing the bounded apply/resume behavior, and adding targeted smoke coverage. Chris remains responsible for review and testing.