Consolidate jabs-project-merge and jabs-features into jabs-cli (KLAUS-566)

[gbeane]

Jira: KLAUS-566

Consolidates two standalone scripts into jabs-cli. Each change is its own commit.

jabs-project-merge → jabs-cli merge

The standalone script and its jabs-project-merge entry point are removed; the logic now lives in src/jabs/scripts/cli/merge_projects.py as a Click command. rich-argparse is dropped as a dependency since that script was its only consumer.

Behavior differences worth reviewing:

• --merge-strategy is still required, but the old unreachable default="destination-wins" (and its misleading "(default: destination-wins)" help text) is gone.
• Project validation now uses Project.is_valid_project_directory(), which checks for both jabs/ and jabs/project.json, instead of only jabs/. The same-project guard compares resolved paths, so ./proj vs proj is now caught.
• Errors surface as Click's Error: ... on stderr (exit 1) rather than the previous rich-formatted ERROR: block.

jabs-features → jabs-cli compute-features

jabs-cli compute-features already existed, and jabs-features already printed a deprecation warning — but it still carried a duplicate argparse parser and its own feature-computation implementation. It is now a thin shim: it keeps the legacy argument surface, warns on stderr, translates the options, and runs compute-features. The duplicated generate_feature_cache() is deleted. The jabs-features entry point stays installed.

The two option surfaces don't line up 1:1, so the shim translates:

• --pose-version was required by the legacy script, so a verbatim passthrough would have broken every existing invocation. The shim accepts it, warns that it is ignored, and drops it — compute-features infers the version from the pose filename.
• Legacy defaulted to pixel units with --use-cm-distances to opt in; compute-features defaults to cm-when-a-scale-exists with --use-pixel-distances to opt out. The shim forwards --use-pixel-distances when --use-cm-distances is absent, preserving the legacy default. One corner is not equivalent: legacy --use-cm-distances on a pose file with no pixel-to-cm scale forced cm settings anyway, where the new command falls back to pixel.
• --window-size N → -w N; --fps and --use-pose-hash pass through. Legacy --fps had no type=, so it forwarded a string into feature computation; the shim parses it as an int.

Docs

• New jabs-cli merge and jabs-cli compute-features reference sections in the user guide, with the jabs-features section replaced by a deprecation note and a legacy→new option mapping table. The ## jabs-features heading is kept so existing anchors still resolve.
• Both copies of the user guide (docs/user-guide/ and the in-app src/jabs/resources/docs/user_guide/) are updated and kept identical.
• In-app user guide nav now points at jabs-cli > compute-features instead of the deprecated script.
• CLAUDE.md and docs/development/development.md command lists updated; jabs-project-merge removed from the "future consolidation candidates" list in the development guide.

Testing

• New tests/scripts/test_merge_projects_cli.py (6 tests) and tests/scripts/test_generate_features.py (7 tests).
• Full root suite passes at both commits (884 at the first, 891 at the tip); ruff check and format clean.
• Smoke tested jabs-features end to end against tests/data/sample_pose_est_v6.h5: per-frame and window_5 Parquet caches written for all 4 identities, and errors from the new command propagate with exit 1.

[Copilot]

Pull request overview

This PR consolidates legacy standalone CLI scripts into the unified jabs-cli entry point, moving project-merge functionality into a Click subcommand and turning jabs-features into a deprecation shim that forwards to jabs-cli compute-features. It updates user/developer documentation and adds test coverage for the new/changed CLI entry points.

Changes:

• Added jabs-cli merge (Click command) and removed the standalone jabs-project-merge script + entry point.
• Reworked jabs-features into a thin shim that warns, translates legacy args, and invokes jabs-cli compute-features.
• Updated docs (both copies) and added new tests for merge + feature-shim behavior; removed rich-argparse dependency.

Reviewed changes

Copilot reviewed 13 out of 14 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
uv.lock	Removes rich-argparse from the resolved dependency set.
pyproject.toml	Drops rich-argparse dependency and removes the jabs-project-merge console script entry point.
src/jabs/scripts/merge_projects.py	Removes the legacy standalone merge script implementation.
src/jabs/scripts/cli/merge_projects.py	Adds new Click-based jabs-cli merge subcommand.
src/jabs/scripts/cli/cli.py	Registers the new merge command with the jabs-cli command group.
src/jabs/scripts/generate_features.py	Converts jabs-features into a deprecation shim that forwards to compute-features.
tests/scripts/test_merge_projects_cli.py	Adds tests for the new jabs-cli merge subcommand.
tests/scripts/test_generate_features.py	Adds tests for legacy→new argument translation and shim behavior.
docs/user-guide/cli-tools.md	Documents deprecation/mapping for jabs-features and adds sections for jabs-cli compute-features and jabs-cli merge.
src/jabs/resources/docs/user_guide/cli-tools.md	Mirrors the user guide doc updates for the in-app documentation copy.
src/jabs/ui/dialogs/user_guide_dialog.py	Updates in-app doc navigation to point to jabs-cli > compute-features.
docs/development/development.md	Updates developer command lists and notes the completed consolidation of merge tooling.
CLAUDE.md	Updates command list examples to prefer the consolidated jabs-cli subcommands.
ruff.toml	Adds per-file docstring rule ignores needed for Click docstring formatting in merge_projects.py.

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