unfortunately it seems to include project specific values e.g. the :Submodules:AndEngine below.

    <facet type="android-gradle" name="Android-Gradle">
      <configuration>
        <option name="GRADLE_PROJECT_PATH" value=":Submodules:AndEngine" />
        <option name="PROJECT_ABSOLUTE_PATH" value="$MODULE_DIR$/../.." />
        <option name="GRADLE_HOME_DIR_PATH" />
      </configuration>
    </facet>

i imagine there's some things to be worked out with how things are setup with gradle and android studio. i'm not sure if they intend the iml files to be committed or not to be honest. i've seen them ignored in other projects... there's nothing really important in them at this point, you can just get it in to your project and working by importing module in the project settings dialog. that said it isn't completely hooked up to the build.gradle and settings.gradle files so there's a couple things you have to do there.

in my case i had to add the following to settings.gradle:

    include ':Submodules:AndEngine'

and the following line to the dependencies section of build.gradle in my app's file:
    
    compile project(':Submodules:AndEngine')

i assume those two tweaks will go away once gradle and android studio are fully cooperating. perhaps they're some tweaks needed to the iml files as well to avoid needing GRADLE_PROJECT_PATH. if i take that out currently gradle barfs on me...