Fixed --keep-prefix functionality.

Changing to keep include prefixes had two side effects: the main
file being parsed wasn't filtered out anymore, and include directory
paths would be added to the path in the include statement.

Also moved the include_test*.fbs files to sub directories so we
can actually test the handling of -I etc.

tested: on Linux.

Change-Id: Ibae095cea7ab0cccbac15cfb5171719f6b5cad8c