Integrate confirmed missing inventory-row pruning into safe workspace cleanup

[chubes4]

Problem

DMC has a safe workspace inventory prune-missing primitive, but workspace cleanup safe does not invoke it. A full safe cleanup can therefore complete successfully while leaving confirmed-absent inventory rows and a persistently noisy hygiene report.

Reproduction

After applying:

studio wp datamachine-code workspace cleanup safe --format=json

workspace hygiene still reported 60 missing inventory paths. The dedicated preview then classified 53 rows for deletion and protected seven present paths:

studio wp datamachine-code workspace inventory prune-missing --dry-run --format=json

Observed summary:

{
  "deleted": 53,
  "skipped": 7,
  "total": 60
}

The pruning primitive was introduced by #869, but operators still need to know and run a separate cleanup surface.

Impact

• safe_workspace_cleanup does not converge workspace hygiene.
• inventory_missing_paths remains noisy after successful cleanup.
• Dead historical primaries look like unresolved workspace problems.
• Operators need undocumented sequencing between cleanup and inventory maintenance.

Expected contract

Safe workspace cleanup should include a bounded missing-inventory reconciliation stage using the existing fresh path and safety checks. Dry-run should report planned row pruning; apply should prune only rows that still pass revalidation.

Acceptance criteria

• workspace cleanup safe --dry-run reports confirmed missing-row candidates and skips.
• Apply rechecks path absence immediately before pruning.
• Rows with protected PR/unpushed evidence retain the existing force boundary.
• Present paths, primaries recreated during cleanup, and ambiguous remote-owned rows are preserved.
• Cleanup evidence reports pruned row count separately from removed worktrees and artifacts.
• A successful safe cleanup converges inventory_missing_paths when no blockers remain.

Related

• workspace inventory: no way to prune orphaned missing_path=1 rows (dead primaries linger, require manual SQL) #869 added the dedicated safe pruning primitive.
• Cleanup planning and bounded safety scans regress on large workspaces #948 tracks large-workspace cleanup planning and bounded-scan latency.

AI assistance

• AI assistance: Yes
• Model: OpenAI openai/gpt-5.6-sol
• Tool: OpenCode
• Used for: live cleanup and prune previews, contract-gap analysis, duplicate search, and issue drafting