For example the sbt-wartremover plugin (added via plugins.sbt with this line: addSbtPlugin("org.brianmckenna" % "sbt-wartremover" % "0.11") )
shows as following in all project .iml files:
<option name="pluginPaths">
<array>
<option value="/Users/epozniansky/.ivy2/cache/org.brianmckenna/wartremover_2.10/jars/wartremover_2.10-0.11.jar"/>
</array>
</option>
I think it should be relative to $USER_HOME instead.