My project conatins several branches, which I keep swapping between.
Once in a while, about once daily, swapping to a branch (not any particular one, happens randomly) would mark all project files yellow. The Project Tree would then only show files directly in the root, and none of the subdirectories:
Though it still sees them in the directory:
Looking through some posts and online, I cannot find a solution that solves this issue. I tried "Invalidating Caches" but that just didn't do anything, restarting also doesn't help.
The only thing that solves this issue when it happens is deleting the .idea directory, then restarting WebStorm, which recreates the directory and apparently re-lists all the files again.
I'd love to resolve this permenantly, if anyone has any idea why this keeps happening.