For me the best solution was to replace Reformat code with Reformat File... Normally when you want to format the code, you hit CTRL+ALT+L. I removed CTRL+ALT+L from Reformat Code and assign it to Reformat File:

And when I hit CTRL+ALT+R, intellijIDEA shows me Reformat File dialog:

Which I can select only changes uncommited to VCS