Do not process files more than once

[iofik]

Hello Scalastyle team!
I have a small, but annoying problem with Scalastyle and SBT plugin.
We use Play framework and what it does by default is setting javaSource and scalaSource SBT variables to the same value ${baseDirectory}/app, which results in unmanagedSourceDirectories and consequently scalastyleSources having this value duplicated. This leads to each file in our Play projects being processed twice. Not only this take additional time, but also results in duplicate error/warning messages in the Scalastyle output.
This can be fixed in multiple places: workaround in our projects, fix to scalastyle-sbt-plugin, and also here in Scalastyle itself. We can make Directory.getFiles method return only unique files (or add corresponding option).
I can create the patch myself, just wanted to get your opinion on where this should be fixed.

[mwz]

Fixed and released here.