Ignored repo inside a project

Hi, I've been using NetBeans for ages and I just migrated (or trying to migrate) to PHP Storm.

Our projects have the following architecture.

/app
/app/something 
/app/something2
/app/inner_repo

And they are connected to repo 1, with "git remote server1".

But, at the same time we have in `.gitignore` of that project the following line:

/app/inner_repo

which is in the folder /app/inner_repo is pointing to repo 2 "git remote server2" - completely unrelated to repo 1. All the changes should be tracked separately.

We don't want any git submodules. We just want to make it work as it works in NetBeans.

We cannot track any changes made to repo 2, because it's obviously ignored. How are we supposed to proceed, please?

Thanks

Edit: added more info about repos