After recent branches pulled, update configs

[hsmaan]

• Currently, different branches have altered the config structure in different ways
• Before merging, ensure that the config structure is up-to-date across configs and with any changes to main

[hsmaan]

Branch merged: guideline tutorials

[hsmaan]

Branch merged: revision figure edits

[hsmaan]

Branch merged: PDAC reannotation

[hsmaan]

Branch merged: Cao et al. balanced trajectory inference

[hsmaan]

Branch merged: umap plots.

This marks all branches used in the main analysis complete. Update for configs/readme pending for this current setup.