Handle removed filtered files better
Handle removed filtered files better

Now use filtering as the *last* step when evaluating whether to remove files. This prevents files that were returned to the graph because other files derive from them to become removed again.

4dn-dcic/fourfront,ENCODE-DCC/snovault,ENCODE-DCC/encoded,ENCODE-DCC/snovault,ENCODE-DCC/snovault,4dn-dcic/fourfront,ENCODE-DCC/encoded,T2DREAM/t2dream-portal,hms-dbmi/fourfront,hms-dbmi/fourfront,T2DREAM/t2dream-portal,4dn-dcic/fourfront,4dn-dcic/fourfront,ENCODE-DCC/encoded,ENCODE-DCC/snovault,ENCODE-DCC/snovault,hms-dbmi/fourfront,hms-dbmi/fourfront,T2DREAM/t2dream-portal,hms-dbmi/fourfront,ENCODE-DCC/encoded,T2DREAM/t2dream-portal