Different repositories for each module in intellij IDEA

You might have to edit the vcs.xml manually:

  • open the vcs.xml of the top module / project

    ex.: ~/[Top module folder]/.idea/vcs.xml
    
  • Add the vcs entry:

    <mapping directory="$USER_HOME$/sub_module01" vcs="Git" />
    <mapping directory="$USER_HOME$/sub_module02" vcs="Git" />
    

Go to Settings/Version Control, there you can configure different VCS roots per directory. So in your case define one VCS root per directory containing the module. You should remove the VCS entry <Project> and just add entries for individual modules so that it looks something like this:

VCS config

If you have files modified in several different repositories and hit CTRL+K or otherwise open the commit dialog all changed files will be selected and when you commit your changes a new commit with the same message will be created in all repositories containing the changed files.

If you want to commit files from just a single module either manually select them in the commit dialog or right click your module, go to Git and select Commit Directory.

To push the commits just hit CTRL+SHIFT+K and you should see something like this (notice that both modules are included).

Push dialog