#429 Core repositories missing markDirty hook — scoped push only works on crash recovery

Description

Three cache-writing repositories do not call the markDirty(relPath) hook before writing to the datastore cache. This means the sync service's per-path dirty tracking (introduced in the Phase 2 S3 extension overhaul, #379) has an incomplete view of what changed during a command. The extension must fall back to a full cache walk on every push instead of walking only dirty directories.

Only UnifiedDataRepository (data artifacts) has the hook wired. The following repositories write to the cache silently:

• YamlOutputRepository — writes to outputs/
• YamlWorkflowRunRepository — writes to workflow-runs/
• YamlEvaluatedDefinitionRepository — writes to definitions-evaluated/

Impact

The Phase 2 S3 extension's scoped push optimization (47x faster walk phase — 142ms → 3ms on 1000-file repos) only activates during crash recovery (when dirty paths are loaded from a persisted sidecar). During normal operation, every push does a full walk because the in-memory dirty set is incomplete — the extension cannot trust it.

Scoped pull (3.9x faster via partitioned index) is unaffected — it uses context.models from the framework, not the dirty set.

Steps to Reproduce

1. Configure an S3 datastore with the Phase 2 extension (dirty sidecar + scoped push)
2. Run swamp model method run on a model that produces outputs
3. Observe that pushChanged does a full walk instead of a scoped walk
4. Enable SWAMP_S3_SYNC_TRACE=1 to see the walk phase timing — it walks all 15 subdirectories, not just the dirty paths

Proposed Fix

Wire the MarkDirtyHook through the three missing repositories, following the same pattern as UnifiedDataRepository:

1. Each repository accepts a MarkDirtyHook parameter in its constructor
2. Each repository calls the hook before every cache write (save, delete)
3. repo_context.ts passes the same hook instance to all four repositories

The hook type (MarkDirtyHook) and the wiring pattern in repo_context.ts already exist — this is extending the existing pattern to cover all cache writers.

Environment

• swamp version: current main
• Affects: @swamp/s3-datastore Phase 2, @swamp/gcs-datastore, any future extension using per-path dirty tracking