Hi Pulkit,
I am no expert, but I think that you have several options:
* Ideally, there would be a flag to your tool telling it to copy or symlink files instead of using hard links,
* alternatively, run your tool in a $TMP directory, and copy back the ones you need in the workspace. This is the wrapper way. Usually a bash script that sets everything up in $TMP, and cleans up after the tool has run.
* patch Tup to support hard links :-). Although in this case it may be very difficult to define a correct semantic for hard links. Not supporting them is probably a feature, not a bug.
Best,
-- Layus