The headless designer command-line you mention in your post will take a
whole Notes Database which has been stored in a source
control system (and this means it has been translated to hundreds of small
files instead of being one monolithic file) and then 'compile' it into an
nsf. I don't think you can do this for a single agent.
If you want the jar files to be available to a single database, then I
am afraid the only way is to do this manually, either into a Java Library
or directly into the agent.
Another possibility which could work if you have access is writing the
JAR files directly into the 'magic' paths on both your server and
your notes client.
However, there are security issues involved because any code which is in
this path is considered absolutely safe and will run without any
restrictions. If you have a godd admin, he will definitely not be happy
about this and will probably want to have a long look at your code.
If your server is at least 8.5.2 then a cool option would be to deploy
your jars as an OSGi bundle (tip from Stephan Wissel, haven't done it