The Plugin folder is not being tracked because GIT thought it was a submodule.
I ran into this issue because I used GIT to clone this Plugin into the plugin directory. and git didnt add it since it was a repository in itself. When GIT didnt add it to my tracked files I did it manually: git add app/Plugin/Migrations/
this created a gitlink and essentially acted like a submodule, as seen in this thread:
Git - how to track untracked content?
Since at the time I didnt want to use the plugin as a submodule, I corrected this issue with the following commands:
git rm --cached app/Plugin/Migrations
with a git status
I could see that GIT was now recognizing my Plugin
I then could proceed with a git add .
and git commit -m "finally adding the plugin"
I hope this helps someone in the future.
Thanks!