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Manuscript files – You'll want a place where you store drafts of the manuscript. This is also where I store the Project Master Document described in Documentation. Store backups of notes here but the active version is on goodnotes on my iPad.  This  This directory is also in a space that collaborators can reach. Some time in the future I might start to store the drafts of the manuscript and other notes in by GitHub Repository and that will mean that I would NOT store these files in a directory that can be accessed by collaborators. Instead, collaborators would pull these files from the repository, but that works only if my manuscripts and notes are text files and not stored as word documents.

Scripts for processing and analyzing data – These are archived using GitHub. Note that each project has a setup script that calls a personal setup script for each collaborator. The personal setup script sets macros for the location of each of the directories on the project. There are some examples of this in the tech tips (but it needs some development).