I am attempting to use tmux from the web based terminal. I am running into the problem that my prefix key seems to be ignored (or, more probably, consumed by the browser or some such). If I ssh into the box, then controlling tmux works just fine. By default I have the prefix key mapped to 'C-\', but it doesn't actually matter. Even with the default 'C-b' keybinding things fail.
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If there are collisions with browser shortcuts, have you tried editing your ~/.tmux.conf file?
https://wiki.archlinux.org/index.php/tmux#Configuration
I also remapped my caps lock key to control key as well which is much nicer IMO:
ajhit406
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