Fix behaviour with removed files

The build test was checking dependencies for deleted files as well
which let to errors. Ignore deleted files.

This fixes the --check-build from
http://logs.openstack.org/86/51386/7/check/gate-openstack-manuals-validate-build/48ad22c/console.html

Change-Id: Id8ee991829cd9f5adefe45a895671f83edb9b04e