Injector surrogate

[roussel-ryan]

This pull request introduces new example notebooks demonstrating usage of surrogate and staged models, updates documentation and references for the Cu Injector model, and makes minor improvements to existing examples for clarity and correctness.

Documentation and Reference Updates:

• Updated the README.md and example scripts to reflect the new location of the Cu Injector model, now under subtrees/lcls_cu_injector_ml_model instead of .submodules/repo. This includes updating the subtree pull command and variable names to use BCTRL instead of BACT for quadrupole controls. [1] [2]

New Example Notebooks:

• Added examples/injector_surrogate.ipynb, a comprehensive notebook demonstrating how to use the InjectorSurrogate model for parameter scans and beam visualization, including quadrupole scans and plotting of beam size evolution.
• Added examples/staged_example.ipynb, which shows how to use the staged model interface, perform quadrupole scans, retrieve and plot image data, and visualize beta functions along the beamline.

Improvements to Existing Examples:

• Updated examples/bmad_model_example.ipynb to remove unnecessary reshaping of the mat6 matrix, simplifying the code for extracting matrix information.

Cu Injector Model Example Script Update:

• Renamed and updated the example script for the Cu Injector model to use the correct input variable name (BCTRL), aligning with the updated model interface.