Git Commit: "Nothing to commit"

but not the changes in the repository.

Please clarify what this means. Why do you expect to see the repository changes reflected in the local FS?

If I open 'Version Control / Local Changes' and then click on 'Refresh' the changes do get picked up.

This makes me think that the local files are being changed by an external tool. When it happens next time, please check if File | Synchronize helps.

I see I wrote something different then I meant with 'but not the changes in the repository' 
I meant that you'd normally see that you've made changes you can check in / commit. However I can see the local changes made to the file when not saved. But not the changes I can check in.

Then files are not changed by an external tool, I make these changes in PHP storm.
When using the same version on windows I do not have this problem. The settings seem to be the same.

Using File / Synchronize does not help.

Somehow the Version Control does not pick up changes unless I click on Refresh, this used to go automatically.

What does `git status` show when PhpStorm doesn't pick up the changes?

Does it depict changed files properly?

Well I tried several things:

- When some new files where added (niet in IDE but on the directory) I can't right click and do git add, as git add is deactivated.
- I am able to run git add to the directory where these files are in, but it doesn't change anything. Running git status shows the files where not added.

- When changing a document in the IDE it does not show the change (by colour) in the IDE, but running git status does show these files where changed.

Nothing weird in the gitignore.
I have this issue with several projects.

I'm experiencing the same issue. Not seeing any help on the help pages, documentation or forums. Weird since it's been years since the first person mentioned this sort of issue on the website. 

@Akulakow Does Git work fine via CLI? Files are not ignored via .gitignore?

What about Settings | Version Control | Ignored Files?