build: do not generate .d file of the uploaded manifest

Fixes #116.

Because modules add files to which cannot be handled by our build
system incremental build fails with messages like this:

  make[1]: *** No rule to make target `/home/tgrabiec/src/osv \
     /apps/cassandra//upstream/jna-3.`

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