[Android] Refine the scripts for generating app packaging tool.

Currently there are lots of issues to generate app packaging tool:
1. Lots of unneeded class files are copied.
2. Two .dex.jar files are not needed by app packaging tool.
3. Some internal Java files like NativeLibraries are compiled when
packaging web apps. They should be handled internally inside of
xwalk runtime.
4. Refine the code for generating app packaging tool.
Fix all above issues with the changes for gyp generation and the
5. Invalid the python file access permission.
generation python tool.

BUG=https://crosswalk-project.org/jira/browse/XWALK-608