No bad idea, especially when turning the Save Stash into a command that would execute without a confirmation dialog. (using always the default message). Maybe it would be useful to split "Save Stash" into "Stash All" and "Stash Selection" (which could show the dialog)?

Do you mean a Git-based issue tracker?

I wonder how this is handled by command line Git users.

Well, the problem in general is unrelated to GitHub Enterprise, but can occur for any in-house repository with proxy access to the internet. Just curious: can't the proxy be configured to also access the intranet servers?

Have you already tried to define an external tool?

SmartGit finds a certain amount of directories that are detected as repositories. What algorithm do you suggest for naming and grouping the repositories - please consider that only one group level is supported and other users might have different structures. Thanks in advance.

The compact view option only is available for read-only Changes views. The File Compare is designed to be freely editable.

In your case I recommend to use a tool that simply fixes all line separators. This is, IMHO, not the task of a version control client.

The 17.1 preview intermediate build 11081 (Help | Check for Latest Build) let's you play with that feature. You can active it from the Changes menu, the option is named "Compact Changes Display".

Just click the Amend checkbox 1 or 2 times.