In the Hamburger menu of the Changes view you can find a "Settings" menu item. There you can select to show all or trailing/selection/changed whitespaces. To make the setting permanent, please use "Remember as Default".

You may give the Standard-window a try for this repository and let me know if you'd like this Pull behavior. Then we can consider to add it (optionally) to the Working Tree and Log window, too.

If a local branch matches its tracked branch in the Standard window, it will be fast-forwarded automatically by pull (even if it had been rebased - just like in the other windows). Could you please explain why you only want to do that selectively?

Just for the records: the Standard-window fast-forwards all tracking branches on Pull. Do you want to get this behavior (optionally) for the Working Tree or Log window, too?

So you mean that "Sort local branches first" should have higher priority than "Sort Refs by Commit Time".

Where exactly the file mode change should be displayed? Could you please create a mock-up of the Changes view?

Quick fix: change the Removed color in the preferences.

I would have changed the paths in repository-grouping.yml and repositories.yml.

Please describe your use-case in more details.