How to handle: Hand-Crafted VS auto-generated VS "manually"-generated files

Clarification:

• hand-crafted: directly edited by humans (a human editing a python or JSON file)
• auto-generated: created as part of a routinely running task (e.g.: a build process generating source-code from templates)
• manually-generated: generated by code, but that code is started manually (e.g. when running git init)

How should we treat these files in a git hosted project:

• Should they be stored in the repo, or (.git)ignored?
• Should they reside in the same folders, or different ones?