[migration] more rename_entity_type fix
* ensure repository caches and system tables are properly cleanup
* delete relations from/to entities deleted through sql
So we don't ends up with a corrupted db...
debian/tmp/usr/lib/PY_VERSION/site-packages/cubicweb/web usr/lib/PY_VERSION/site-packages/cubicweb
debian/tmp/usr/share/cubicweb/cubes/shared/data usr/share/cubicweb/cubes/shared
debian/tmp/usr/share/cubicweb/cubes/shared/wdoc usr/share/cubicweb/cubes/shared