API: Remove fly-dimension from arrays

[carterbox]

Purpose

Remove the 'fly' dimension from arrays because it is not being used. I plan to replace this dimension with the 'coherent' probe dimension which is necessary for orthogonal probe relaxation.

Approach

Removed the fly-dimension from documentation. Also, improved the tests for ptycho algorithms to provide better feedback by actually saving the results to the disk. By looking at the results, I already squashed a bug where lstsq_grad probe recovery wasn't working correctly.

Pre-Merge Checklists

Submitter

• [x] Write a helpfully descriptive pull request title.
• [x] Organize changes into logically grouped commits with descriptive commit messages.
• [x] Document all new functions.
• [x] Write tests for new functions or explain why they are not needed.
• [ ] Build the documentation successfully
• [x] Use yapf to format python code.

Reviewer

• [ ] Actually read all of the code.
• [ ] Run the new code yourself.
• [ ] Write a summary of the changes as you understand them.
• [ ] Thank the submitter.