[gbradham]

Fixes all eight open issues, one commit per issue (four for #212).

Closes #205
Closes #206
Closes #207
Closes #208
Closes #209
Closes #210
Closes #211
Closes #212

Changes

• Maimu Plugin Install Concurrency #205 Plugin nodes need a restart: the node library listed plugin nodes only once, when it was built. The Plugins window now emits plugins_changed after an install, enable or reload, and the main window rebuilds the library on it.
• Package installs in app #206 Package installs in app: unavailable Analyze cards get an Install button. It installs the requirements GLIDER's own metadata lists for the extra (installer.extra_requirements), not glider[extra], which would resolve the unrelated glider project on PyPI. Then it offers a restart, because the availability probes are memoized. The relaunch runs at interpreter exit, so serial ports are released first. Frozen builds get no button.
• Rename "mice" to "animals" #207 Mice → Animals: renamed the section, its key, its icon file and the placeholder text.
• Remove "Files" tab on desktop #208 Files tab: removed from the desktop Builder; the runner's Files tab is unchanged.
• Leftover behavioral prediction cleanup #209 Live behaviour labels: removed BehaviorAnalyzer, its overlay, its settings and the behavioral_state column from new tracking CSVs. velocity_px_frame is kept, now computed as the mean step length over the trail. Analysis already treats behavioral_state as optional, so old recordings still load.
• Shortcut menu fix #210 Ctrl+K on Mac: palette shortcuts and the status-strip hint render as native text (⌘K on macOS).
• Batch Pose above Behavior Analysis #211 Order: Batch Pose Tracking is listed above Behavior Analysis, in both the Analyze tab and the Tools menu.
• Arena calibration #212 Arena replaces calibration:
  • Round arenas: ArenaCalibration gains shape="ellipse". An ellipse is the affine image of a circle, so the existing homography is reused: the corners are the ellipse's bounding parallelogram. Only containment (outside_cm, used by the arena gate) and the centre zone know the arena is round.
  • Dialog: a Rectangle/Circle choice and separate width and height. A circle is drawn as a centre plus two edge points. Reopening an arena no longer loses its height.
  • Arena is the scale everywhere:
    • Batch Pose drops Calibrate… and Copy to Selected.
    • Camera Settings now has Arena… instead of Open Calibration… (desktop and Pi). The live arena is saved in QSettings.
    • Pup-retrieval Set scale… uses the arena dialog.
  • Tracking logger: ArenaCalibration provides the scalar interface the logger reads, so the CSV headers and distance_mm are unchanged.
  • Scale readers: _borrow_from_folder_mate and calibration_spread_warning now also read arenas.
  • Removed code: the line-drawing CalibrationDialog is deleted. CameraCalibration stays, so old master files still load.
  • Known limits: a circle is fitted as an ellipse, without full perspective correction, and the misplaced-corner warning only applies to rectangles.

Docs are updated for the Builder window, tracking, the camera arena section and pup retrieval.

Testing

• Full suite: QT_QPA_PLATFORM=offscreen uv run --no-sync pytest -q -m "not slow" gives 6674 passed, 4 skipped, 7 deselected. That is below the pre-Arena calibration #212 run on this branch (6696) because the deleted calibration dialog's test file and the seven line-copy tests went with it.
• ruff check and black --check are clean on src tests plugins tools.
• New tests:
  • the install signal (Maimu Plugin Install Concurrency #205)
  • the install button and extra resolution (Package installs in app #206)
  • velocity smoothing (Leftover behavioral prediction cleanup #209)
  • native shortcut text (Shortcut menu fix #210)
  • ellipse arenas: scale, containment, round trip, logger interface and the dialog (Arena calibration #212)
  • borrowing scale from an arena-only folder-mate (Arena calibration #212)
• The circle-mode dialog was rendered offscreen and checked visually.