You can delete those.. Or after migration to crx3 and before upgrade can follow below steps for clean structure. i use cp instead of move to take care of any upgrade issue.
mv crx-quickstart crx-quickstart.cq
mkdir -p crx-quickstart/repository/repository
java -jar aem-author-p4502.jar -unpack
cp -R crx-quickstart.cq/install crx-quickstart/install
cp -R crx-quickstart.cq/repository/segmentstore crx-quickstart/repository/segmentstore
cp -R crx-quickstart.cq/repository/repository/datastore crx-quickstart/repository/repository/datastore
echo Start AEM 6.1
java -Xmx4G -Xms4G -XX:MaxPermSize=2G -XX:PermSize=2G -jar aem-author-p4502.jar -r author,crx3,crx3tar
once everything is fine delete crx-quickstart.cq