Take a look at the idea plugin, we use it to automatically download Javadocs 
and sources

http://gradle.org/docs/current/userguide/idea_plugin.html

For specific local directories you might have to specify a project library 
which probably can help to provide such data while generates that XML file, not 
sure if that interferes with regular dependencies management 

http://gradle.org/docs/current/dsl/org.gradle.plugins.ide.idea.model.IdeaProject.html#org.gradle.plugins.ide.idea.model.IdeaProject:projectLibraries

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