In merging code branches, it would be immensely helpful to be able to do a reconciliation with the ability to mark files as "reconciled" even though they may not match exactly. It would be even better for this to be remembered in a 'project' file for the folder comparison so that the two branches could be periodically compared without having to reconcile files previously marked as reconciled which have not changed in either branch since the last reconciliation.

It would also be very helpful to include the ability to map files that have different names or different paths to each other. Two examples of reasons this is useful: 1) prior developers who can't spell named the files, and the file/classnames have been corrected 2) prior developers put code in the wrong layer/project of the solution and the code needed to be moved to a layer that could be accessed by more of the solution's projects. Right now, to compare these, I have to manually select the two files each time and select compare from the context menu. PITA when comparing thousands of different files in two branches.

And just because it hasn't been said enough.. three-way folder merge please!