Fix: False Positive Nested Catalog Recreation Warning

The new implementation of `.cvmfsdirtab` does warn the user about the manual removal of nested catalog markers in auto-generated nested catalogs. However, the check for this warning didn't check for the actual marker to be removed but only for the directory to show up in the scratch area. This resulted in false positive warnings when the content of an auto-generated nested catalog was modified without removing the `.cvmfscatalog` file. The bug does not produce any other issues despite possible user confusion.

**Note:** Additionally this contains a regression test for the bug being fixed.