fpm sometimes does not properly rebuild the project when module internals are changed

I don't have a minimal reproducer yet, but a few times this fails:
```
fpm run
```
And this fixes it:
```
fpm clean
fpm run
```

I am opening up an issue for this, as there is almost for sure a bug in fpm, I just have to create a reproducer and then we can work on fixing it and adding a test for this.