I came to git/Sourcetree from svn/TortoiseSVN. One of the nice features of Tortoise and other SVN clients is that you could configure the client to prompt for an issue tracker ID. This was especially useful for linking commits to JIRA tasks, and having the prompt ensured that team members tracked their commits to JIRA issues.
Sourcetree doesn't seem to support this. Human behavior being what it is, our team often forgets to enter JIRA IDs in their commit messages. We have the JIRA/Github integration turned on, and use that to automatically transition tasks. Without those JIRA ids, the integration isn't that effective.
Any plans to add this feature to Sourcetree?