The issue of merging directories is actually quite different from that of merging files.
Let's note that, under ClearCase, directories are not stored in containers (standard file objects found in vob pools) unlike file elements, so that their merging cannot be delegated to external tools, acting upon inodes accessed over NFS. It has to use ClearCase functions at the low level, to create and remove hard links.
In fact, with large directories, it is often more convenient and more manageable to use
ln explicitly than to use
merge, and correct the results before checking in:
$ ct co -nc -bra /main . cleartool: Warning: Version checked out ("/main/6") is different from ### version selected by view before checkout ("/main/mg/3"). ...