I'm using Intellij IDEA 14.1.4 on OpenSUSE 13.1 linux. I recently changed from working on a svn-based project to a git hosted project. I know virtually nothing about git command line and just use intellij's built in git tools.
The problem is the project frequently forgets which project files have been modified. The files will become listed as black in the file tree, and do not appear when I go to VCS -> Show Changes View. If I edit the file and modify a single character, then all the modifications to that file suddenly appear, it turns blue in the file tree and shows up in the Show Changes View. I will go on to make other changes in other files, and at some point the same file will turn back to black in the tree and not show in the show changes view.
I've deleted/recreated my project and deleted the projected folder and re-checked out the files from git. Rebuilding indexes has no effect. Sometimes restarting will cause files to suddenly appear in the change list. It happens on a minute by minute basis. To the best of my knowledge no other program/process is touching my project files, and it doesn't happen to an svn based project I have on the same file system. I've tried removing the git package from my linux system and that made no difference.
Any guesses as to what is going on?