By default the directory based replica catalog backend constructs deep lfn's while traversing an input directory.

For example
if input directory is input
then
input/deep/f.a file results in LFN called deep/f.a

If a user sets,
pegasus.catalog.replica.directory.flat.lfn to true

then the leaf is only constructed for creating the lfn.
example
input/deep/f.a will result in lfn f.a