To diagnose it, follow this answer.
But to fix it, knowing you are the only one changing it, do:
1 - backup your project (I did only the files on git, ./src folder)
2 - git pull
3 - restore you backup over the many "messed" files (with merge indicators)
I tried git pull -s recursive -X ours
but didnt work the way I wanted, it could be an option tho, but backup first!!!
Make sure the differences/changes (at git gui) are none. This is my case, there is nothing to merge at all, but github keeps saying I should merge...