Can you install NPM and Git under a standard user account

I think that a package manager will do most of what you need. I will show macports as that is the one I know but the others have similar functionality.

If you use the standard packages ie the up to date ones that have been packaged then macports will do all the dependencies for you. e.g. building scipy knows it has to build numpy first and will do it. You can also ninstall a port easily - macports will tell you if any ports depend on it. If a port is chnaged then macports will update the ports depending on it.

You can also manually chnage the port to deal with development versions of numpy for example. You will have to produce a copy of the port file and edit that see macports guide. The minimum would be to change the version and the rules for downloading so you get different code but can include many patches for OSX specific functions.

You can keep track of what you have installed by port list (also more advanced calls to minimise the number of commands you need. The changes you made will be in your local Portfile repository which will need to be backed up and a small change to the defualt macports config made.

Git is a version control system and stores the history in a subdirectory .git

That is a way of keeping copies of snapshots source code or other documents in a way so that you can go to the complete set of documents at an earlier given time and/or see when and who changed a file and what change was made.

A version control system can be used just for your documents or put in a shared place so people who collaborate all can see and make changes.

You can use tools like SourceTree to view what is in your history.

Thus is you are not using git you can delete the .git directory but I would ask how did it get there. It is possible that another application could use git, I would see if any of your apps say they keep old copies of data however I would hope that they would not do this for all of ~/Documents as this would mess up other peoples' use of this directory. The actual directory .git is in would help to identify the application using it.