How to add native library dependencies to sbt project?

You should replace the %% (double percent) with single one.

libraryDependencies += "org.apache.pdfbox" % "pdfbox" % "1.8.2"

The double-percent is a convenience operator, and causes adding the _+scalaVersion postfix inside the path, which is _2.10 in your case. Single percent should fix the problem.