Merge 05 with 05.1 and 05.2 and some of 10

Fixed path
Added threshold constants
Added filtering and plot designation skeleton
Added additional columns to adata, but they should still be processed more before merging with 10 and reran
Removed some memory shortcuts that are no longer needed with more knowledge on server job submissions
Typos
Noted that annotation should happen first and filtering should happen last
WIP Need to relogic the actual filtering booleans to match the annotation changes
Added 05.2's annotation logic in comments that needs to be re-approved
Made 'clean_markers' function to reduce clutter in plotting portions
Renamed curated/manual data objects to better match their use