Your comments
Explanation: SmartGit always is very sensitive to what control has the focus and what is selected. The Query | Show Changes menu item (= toolbar button) requires the focus in the Files view and a single selection there.
We could relax this a little bit to not require the focus in the Files view.
Please vote for request 988.
You either can ignore untracked files or mark tracked files as 'Assume Unchanged' or 'Skip Worktree'. You can find such commands in the Local menu.
Show Issue Numbers in log view that relate to commits (next to authors)/em>
This should already work (for any issue tracker): https://www.syntevo.com/doc/pages/viewpage.action?pageId=1704589
Regarding the other suggestions, I reckon you want to get something like the JIRA integration: http://www.syntevo.com/doc/display/SG/JIRA?
Wouldn't an issue tracker or a tiny todo.txt file be the better choice? IMHO, it is not the task of a version control client to support every part of the development workflow.
Customer support service by UserEcho
What benefit would have the in-place copy/rename?
Regarding the Shift+F5 default shortcut for Create Link: what other shortcut do you suggest? I'd consider it is some kind of lightweight copying.