Correct the documented on-disk annotation file format

[gbeane]

Reasoning

I went looking for a bug first and did not find one I was confident in, so I picked the next
category: misleading documentation. The docstring on
VideoLabels.as_dict
is the only place in the tree that documents the layout of a project's
jabs/annotations/<video>.json file, so anyone reading a JABS annotation file from an external
tool ends up here. It was wrong in four ways:

1. A key that does not exist. The example showed a timeline annotation's optional identity
   field as "animal_id": 0. The actual key written by
   TimelineAnnotations.serialize
   is "identity". animal_id appears nowhere else in src/ or packages/ -- a consumer
   following the docstring would silently never find the identity.
2. The external_identities example was malformed and backwards. It read
   "external_identities: { "jabs identity", 1234, } -- an unterminated key and a comma instead
   of a colon -- and implied the mapping went from a name to a number. The code writes
   {str(jabs_identity_index): external_identity}.
3. version was undocumented. as_dict has written a "version" key
   (SERIALIZED_VERSION) since it was added, but the example never showed it.
4. labels vs unfragmented_labels was unexplained. Both were shown with byte-identical
   contents, which reads as pointless duplication. In fact labels is masked by
   pose.identity_mask() (blocks split where the identity is absent from the pose file) while
   unfragmented_labels is what the user actually labeled, and load() prefers
   unfragmented_labels. That distinction is the single most important thing about this format
   and it was missing.

This is safe because it is comments only: no statement, expression, signature, or default was
touched, so behavior is net-zero by construction. Nothing in the tree parses these docstrings.

Change

Logic changes

None -- every edit is inside a docstring.

Documentation changes

• src/jabs/project/video_labels.py -- rewrote the as_dict docstring. It now has proper
  Args/Returns sections, documents each top-level key (including version), spells out the
  labels / unfragmented_labels difference and which one load() prefers, notes that
  external_identities and annotations are only present conditionally, points at
  TimelineAnnotations.serialize for annotation entry fields, and carries a valid JSON example
  with "identity" instead of "animal_id".
• src/jabs/project/timeline_annotations.py -- documented the serialized fields of one
  annotation (start, end, tag, color, optional description, optional identity) on
  serialize(), where they are produced, and noted that the derived display_identity is not
  serialized because load() recomputes it.
• packages/jabs-core/src/jabs/core/abstract/pose_est.py -- corrected the
  external_identities entry in the PoseEstimation class docstring: the property is annotated
  and populated as list[str] | None, not list[int] | None (the v4+ readers stringify the raw
  ids).

No mechanical/import churn in this PR.

Verification

• uv run --only-group lint ruff check -- all checks passed
• uv run --only-group lint ruff format --check -- 460 files already formatted
• uv run pytest -- 879 passed, 254 skipped
• uv run pytest packages/jabs-core/tests -- 88 passed

🤖 Generated with Claude Code

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Generated by Claude Code

[Copilot]

🟢 Approval recommended

Documentation-only updates align with current serialization behavior, and the remaining feedback is a minor clarity nit.

Pull request overview

This PR corrects and clarifies the documented on-disk JSON format for JABS per-video annotation files (jabs/annotations/<video>.json) by updating the relevant docstrings to match what the code actually serializes/deserializes.

Changes:

• Rewrites VideoLabels.as_dict() docstring to accurately document top-level keys (including version), fix the identity key name (identity), and explain labels vs unfragmented_labels.
• Documents the serialized fields produced by TimelineAnnotations.serialize() and consumed by TimelineAnnotations.load().
• Fixes the PoseEstimation docstring type/meaning of external_identities to reflect list[str] | None.

File summaries

File	Description
src/jabs/project/video_labels.py	Updates as_dict() docstring to match the real JSON annotation file structure and key semantics.
src/jabs/project/timeline_annotations.py	Documents the serialized annotation entry fields and clarifies what is (and isn’t) persisted.
packages/jabs-core/src/jabs/core/abstract/pose_est.py	Corrects external_identities docstring to `list[str]

Review details

• Files reviewed: 3/3 changed files
• Comments generated: 1
• Review effort level: Lite

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