It looks like the relax application has been jd2 for over a year now, so the standard flags for controlling silent file input with jd2 (such as -in:file:tags) should also work with the relax application directly (at least for 3.2 and 3.3) – no need to split them off into a separate file first.
One clarification, though. From my reading of the code, -in:file:tags takes the list of tags themselves, rather than taking a filename of a file containing the list of tags. If you’re using a bash-like shell to run the job, though, it’s easy enough to work around that. Just do something like “-in:file:tags `cat listoftags.txt`”, where it’s backticks around the “cat” command. (The backticks tell bash to run the command and place the output on the command line in its place.)