module.py: move test.manifest.gen processing out of jvm class

Processing of this manifest was inside JVM-specific code which caused
the manifest was not processed if there was no java application
in the image.

For example:

  make image=empty check
  ...
  run_main(): cannot execute tests/tst-af-local.so. Powering off.
  Test tst-af-local.so FAILED
  make: *** [check] Error 1

Let's move it to the main manifest processing function.

Signed-off-by: Tomasz Grabiec <tgrabiec@cloudius-systems.com>
Signed-off-by: Pekka Enberg <penberg@cloudius-systems.com>