once you're in that tab of the dialog, create a new filter called something like:
binary-code
and add these folder names as values for the filter:
- bin bin.ant bin.eclipse subprojects bin-eclipse codegen genned-src genned-obj unit-test-reports
+ bin.ant bin.eclipse subprojects bin-eclipse codegen genned-src genned-obj unit-test-reports
any directory listed there will be ignored during comparisons and merges, which is
more convenient than the alternative of seeing all the binaries that are different,