PHP's default session handler stores the session data in serialize() format in a file, which means it's basically plain-text. You could certainly manipulate that file from the command line, using any of the standard unix text manipulation tools (perl, sed, awk, even echo/cat in a shell script, etc...), as long as you don't introduce a syntax error into the serialized data.
But at that point, unless you find a function/library/module that does unserialize() and most likely serialize() as well, you might as well just PHP itself to do the manipulation. It'd be a pretty rare system that doesn't have the CLI version of PHP installed alongside the webserver version.
$dat = file_get_contents('/path/to/session/file');
$session = unserialize($dat);
$session['temp'] = 'whatever';
$dat = serialize($session);
file_put_contents('/path/to/session/file', $dat);