Implement A la carte updating of JGI data

[colemathis]

• Rename jgi_ko_edit.py to jgi.py and delete or jgi.py (we'll handle the diffs when we merge)
• Change function names to reflect the fact that they'll actually be public now (e.g. remove leading _ or unsafe. If it expected to be public just add "safety" cavets to docstrings.
• Make sure docstrings are clear and updated (use ChatGPT as needed).
• Finalize documentation of how to use A la carte functionality.
• Include a working example in the example directory with very detailed instructions, for pulling just EC data and for EC + KO data