How do I use the command line interface to make stream copy? And what if I want to have the copy in another format?
It can be done, I suppose. Easier would be using scripting + command line and a saved job and modify that job to suite your needs. Create job in Avidemux GUI to your need and save that one.
Info can be found here: Avidemux wiki: Scripting tutorial (http://www.avidemux.org/admWiki/doku.php?id=tutorial:scripting_tutorial)
Very basic sample using above: 2.6 audio track switching in job.py (http://www.avidemux.org/smf/index.php?topic=10499.0)
If you just want command line: Avidemux wiki: Command line usage (http://www.avidemux.org/admWiki/doku.php?id=using:command_line_usage)
Other stuff users wrote: Documentation & Tips (http://www.avidemux.org/smf/index.php?board=10.0)