Depending upon what kind of access you need to your linux env, as a stopgap, maybe you (the wanting linux users) could use ManicTime from a separate Windows box which serves as little more than an X Windows Server terminal.
I'm assuming that there is some Windows X-Server that will properly convey the window titles of your various remote linux application to the Windows desktop. Combined with the window title parsing capability in ManicTime, you may even be able to extract some "Document" info. It would also not seem to be limited to use on Linux, but SunOS, HP, whatever.
Aesthetically displeasing as I'm sure it would be, maybe even from a unix-based Mac, too? :)