fixes #3: JarInputStream assumes that the first entry is the manifest.

I had an issue with one jar file that had the manifest not at the
beginning. Therefore now I use JarFile instead of JarInputStream
and manually filter the manifest on copying.
Fix test run on travis
fixes #4, fixes #5: also add dependencies added with fileTree
Don't use version based download for SNAPSHOT dependencies
inputs.removed fixed
Tests run on Windows as well