Log Cell Annotation store initialization and tighten scaffolding coverage

[Copilot]

This PR completes the remaining scaffolding for the Cell Annotation plugin lifecycle: when the feature flag is enabled, dataset open now emits the resolved .UELer store path, and the storage tests cover the expected atomic-write and persistence guarantees more explicitly.

• Plugin lifecycle

  • Log the resolved dataset store path from CellAnnotationPlugin.on_dataset_opened().
  • Accept ENABLE_CELL_ANNOTATION=on in addition to the existing truthy flag values.

• Atomic storage semantics

  • Extend coverage to assert atomic_write_json() does not leave visible temp files after a successful replace.
  • Extend coverage to assert atomic_replace() fsyncs both the source and destination directories around os.replace().

• Scaffolding behavior coverage

  • Add focused coverage for dataset-open logging so the plugin’s checkpoint/store initialization is externally visible when enabled.

Example of the plugin-open signal added here:

def on_dataset_opened(self, base_folder: str | Path) -> None:
    self._store = DatasetStore(base_folder)
    self._store.ensure_dirs()
    self._manifest = Manifest(self._store.store_path)
    if self._manifest.load() is None:
        self._manifest.rebuild_from_disk()
    logger.info("[CellAnnotation] dataset store ready: %s", self._store.store_path)

Original prompt

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This section details on the original issue you should resolve

<issue_title>Sub-issue: Plugin Scaffolding — Cell Annotation + Storage</issue_title>
<issue_description># Plugin: Create Cell Annotation plugin skeleton & storage scaffolding

Tracked by: #15
Milestone: M1 — Scaffolding
Labels: area:cell-annotation, area:storage, type:infra, size:M, priority:P1

Summary

Add a new Cell Annotation plugin that owns checkpoint orchestration and .UELer persistence. Provide storage helpers and lifecycle hooks so the plugin initializes per-dataset folders.

Scope

In

• New package viewer/plugins/cell_annotation/
  • plugin.py: orchestrator class, event hooks (on_dataset_opened/closed)
  • store.py: .UELer resolver, dataset ID hashing, atomic write helpers (temp → fsync → os.replace)
  • manifest.py: thin wrapper (stub for now) with load(), save_atomic(), rebuild_from_disk()
• Wire plugin registration into the viewer bootstrap so it’s available behind a feature flag

Out

• No UI yet (browser, dialogs)
• No AnnData serialization (handled in Serializer sub-issue)

Deliverables

• plugins/cell_annotation/{__init__.py,plugin.py,store.py,manifest.py}
• Feature flag: ENABLE_CELL_ANNOTATION (env/config) gates registration
• Dataset-level folders on open:

.UELer/dataset_<stable-id>/
checkpoints/
thumbnails/
selections/
manifest.json (may not exist yet)

• Atomic write helper functions:
• atomic_write_json(path, obj)
• atomic_replace(src_tmp, dst_final) (fsync file + dir)

Acceptance Criteria

• With flag on, plugin loads and logs dataset store path on open
• .UELer/dataset_<stable-id>/{checkpoints,thumbnails,selections} created if missing
• atomic_write_json() writes a file recoverable after simulated crash (no partials left visible)
• With flag off, plugin does not register; app runs unchanged

Test Plan

• Unit: store path resolution from dataset root; atomic write semantics (fsync + replace)
• Integration: open dataset → folders exist; toggle flag on/off
• Windows path test: ensure no file handle leaks; partial files ignored by future scans

Dependencies

• Tracked by Epic: Cell Annotation Workflow (checkpoints, merge, flexible markers) #15
• Blocks: Interfaces (Sub-issue: Cross-Plugin Interfaces & Registration #17), Serializer (Sub-issue: AnnData Serializer, Schema & Validator #18 )
  </issue_description>

<agent_instructions>This is a sub-issue of Issue #15</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Sub-issue: Plugin Scaffolding — Cell Annotation + Storage #16

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