Screen and Tmux can help a little, but not much (if my work involved stable configurations of tabs, I could save maybe 2 minutes of setup per reboot). Unless you're proposing running all command line tools only on remote servers, which won't work with local files.

I think the problem already has a solution: no automatic reboots. Tell me it's needed and I'll sigh, do what I need to to save my state, then do it myself.