In Kaleidoscope, how do I configure it to ignore whitespaces?
I emailed the support team and the answer is:
As of Kaleidoscope 1.1.2, there is no way to ignore whitespace in Kaleidoscope.
Also see this tweet
Kaleidoscope 2.1 beta has the "ignore whitespace" feature. It is on the bottom toolbar. See: http://www.kaleidoscopeapp.com/beta
You may want to look at http://kdiff3.sourceforge.net/ for a free alternative that runs on OS X and supports many more functions than Kaleidoscope.
KDiff3 obviously doesn't have as fancy of an interface, but it works well and supports all the things Kaleidoscope is still lacking, like merging and whitespace/line ending ignoring.