I don't think any of the three problem areas are intrinsic to gui or cli The rename aspect is a problem in both cases and is related to how git works internal

I don't think any of the three problem areas are intrinsic to gui or cli The rename aspect is a problem in both cases and is related to how git works internally. Dirty commits van be really useful for the above, do a commit to rename, then another to modify. That keeps the rename operation clean and modifications in their own diff. For workflow, that is a team process and documentation problem. Every team should document the typical CLI commands for their workflow. Having no documentation around this is negligent, simply referencing some webpage is lazy, it should be spelled out for you