Update missing derived_from detection
Update missing derived_from detection

Don’t mark derived_from files as removed from the graph because there can be many copies of each derived_from file. Now just use the given files array to note removed files.

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