Restore JGIT 2.x stream.

It is impossible to build SDK with JGIT 3.x, and due to the short
deadlines it is not advised to do a migration right now.
Remove jar duplicates.

Due to the inconsistencies in the target platform management, some
bundles are duplicated. This patch filters out duplicates, as we don't
care about OSGi requirement, because it's all classpath in the SDK tool.
Fix hang on Linux.

The problem is caused by the fact that shell resolves "*" classpath
variable in a pretty random order, sometimes causing hangs or other
exceptions, because jars were loaded/initialized in a wrong order. This
patch enforces strict jars ordering. "head -1" is to ensure that one
osgi bundle in two different versions will not break the classpath
(because ls would return then two lines).