I use the idea plugin on several large projects regularly, and when dependencies change simply run 'ideaModule' again. Once upon a time that took quite awhile, but the last couple of versions of Gradle have significantly sped things up, to the point where it's now basically on par with Intellij re-importing a changed maven pom. Another bonus to using the plugin is that you can automatically attach source and javadoc for dependencies in your IDE - something that you won't have if you just refer to a flat 'lib' directory.
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