Try using Sysinternals Disk Usage (otherwise know as du), specifically using the -u and -v flags will only count unique occurrences, and will show the usage of each folder as it goes along.
As far as I know the file system doesn't show the difference between the original file and a hard link (that is really the point of a hard link) so you can't discount them on a folder-by-folder basis, but need to do this comparatively.
To test I created a random folder with 6 files in to. Cloned the whole thing. Then created several hard and soft links inside the first folder to reference other files in the first folder, and also some in the second.
Running du -u -v testFld results in (note the values next to the folders are in KiB):
104 <path>\testFld\A
54 <path>\testFld\B
149 <path>\testFld
Totals:
Files: 12
Directories: 2
Size: 162,794 bytes
Size on disk: 162,794 bytes
Running du -u -v testFld\a results in:
104 <path>\testFld\a
...
Running du -u -v testFld\b results in:
74 <path>\testFld\b
...
Notice the mismatch?
The symlinks in A that refer to files in B are only counted against A during the "full" run, and B only returns 54 (even though the files were originally in B and hard-linked from A). When you measure B seperately (or, if you don't use the -u unique flag) it will count its "full" measure of 74.
Best Answer
cmdincludes themklinkcommand which can create hardlinks:Furthermore, the excellent Far Manager has support for creating them (Alt+F6).
There are also a number of shell extensions that allow for doing so.