I have, once again, explored the limits of stupidity. I have two directories, we'll call them D1 and D2. D1 is where I originally developed the application and where the git repository was set up. I also created a remote repository on github. When I changed IDE's, I copied D1 to a new directory, D2, and ported the project to Android Studio. Then, being an idiot, I proceeded to make lots of changes to the code in D2, to get the code to compile under Android Studio and run under Android Nougat.
Now, I have a bunch of files in D2 that are updated versions of the files in D1 and I want the repository to be updated and preferably move the repository to D2. I'm still fairly inexperienced with Git. How can I do this safely?
Additional Info 11/27/2017
The directory layout in D1 is for Eclipse/ADT, but the layout for D2 is Android Studio. The directory trees are different. So one of the ideas I was hoping would work, copying the git directories, won't. It looks like I'm going to have to try copying the source files, except then I still have the problem that when I do a clone, the directory structure won't be correct for Android Studio. Or am I completely missing something?
I did some more digging and found this post which means, I think, that it should be safe for me to move directories around in a repo.
Can Git restructure my folders without losing history?
Thanks for helping!