How to disable change caching intellij idea 2016_1 CE?

Question

git

Perhaps earlier, but starting from version 2016.1, the idea began to cache the change in raw files. I use GIt, and it often happens that I made changes, I check in the terminal emulator with the git status command, and git does not see the changes, but at the same time, the Idea marks the changed lines as expected. With a long enough work, it may turn out that the Idea marks all the changed lines, but not everything is reset in the FS (my guesses) and as a result, when committing, not all changes get into the rep. How to disable this feature bug?