Is there any way to change the default settings for BBEDit so that when it launches in as the "Diff Tool" or "Merge Tool" (compare-file mode) from Git Tower or other apps, it will ignore
leading and trailing whitespace? When comparing from the 'Search' -> 'Find Differences' menu there are checkboxes for these settings.
Once the diff is launched I don't see any way to change them and recalculate the diffs.
This could be managed with a preference, or global environment variable before the app launches, or ideally an option click on the 'recalculate' button, or a checkbox that can be clicked after the app is launched.

If there's a way to do this from the BBEdit command line tools API, it might be possible for me to intercept what Tower is doing to launch it, but I imagine that will be difficult and not survive upgrades.
This is an essential feature. Please let me know if there's a way to do it or if it can be added.
It would also be very valuable to have control over ignoring line ending differences (Unix/Mac; CR, LF, CRLF) in this context as well.
An alternative I've found is to use Kaleidoscope, which has a check box for this, but doesn't let you edit the files directly, so I'd have to go back and forth between BBEdit and Kaleidoscope, and it wouldn't work well.