Monitor modernization + few cleanups and fixes

[ShantanuKodgirwar]

What and why

Modernizes the reconstruction monitor that every engine uses, and fixes issues found along the way.

• New interface: engines pass one MonitorFrame per update to monitor.update(frame). Cropping and FPM handling moved from BaseEngine into the monitor. Existing monitors keep working through the old hooks.
• Jupyter: figures update in place instead of the cell being cleared, and progress bars use tqdm.auto, so they no longer print a line per iteration.
• New figures and saving:
  • A parameter-history figure (zo, theta, purity, scan positions), shown only for quantities that change.
  • reconstruction.saveResults(..., snapshot=monitor) and monitor.saveFigures() save PNGs of the final figures.
• Quieter logs: per-iteration messages are logged once, and the error/overlap summary prints at the end of the run.
• Fixes:
  • DummyMonitor crashed with TV_autofocus on.
  • ePIE never updated the monitor.
  • NapariMonitor used the wrong layer name.
  • The error plot was squeezed and had overlapping ticks.
  • HDF5 files are now closed with with.
• Cleanup: removed dead code and unused hooks, BaseEngine-style docstrings, Literal type hints, no more global warning filter.

How it was tested

• 136 passed, 17 skipped, including new tests/Monitor/ tests. The engine regression goldens are unchanged.
• Checked live in Jupyter, VS Code # %% cells and a GUI window, plus an FPM run, using example_scripts/exampleMonitorGUI.py.

Notes

None