Prepare for Freesurfer Merge

We need to get the code in a state that we can merge it into the main free surfer repository and replace the existing MATLAB implementation.

Action items are:

Merge main freesurfer branch to check for any conflicts.
Make sure there have been no MATLAB ode changes
Work on Dev mode README to streamline the following tasks
- GEMS C++ code changes should just be a matter of running make inside the GEMS directory without any additional pip installs
- Modifying Python code should just be a matter of editing the Python files without additional pip installs
rename as_python to samseg and remove existing MATLAB code.

innolitics / freesurfer