Bob answered this on the mailing list, but I'll paste it here as well:
You can deploy pure Java applications on TorqueBox, but you don't use
a torquebox.yml (or *-knob.yml).
To deploy a Java application in TorqueBox, just drop your .war file
into the apps/ directory directly (I'm assuming TorqueBox 1.x)
fwiw, if deploying a Ruby application, you can put a torquebox.yml
inside your application, but the files in app/ would be a *-knob.yml
file, or an archived version of your application with the extension of
.knob.
When we refer to "knobs", we mean either the *-knob.yml, or the *.knob
archives, which are used in the apps/ folder. torquebox.yml is
primarily used within your application's own directory tree.
For Java applications, ignore everything TorqueBox-related, and you
can pretend that our distribution is just like JBoss AS6 (for
TorqueBox 1.x) or just like JBoss AS7 (for TorqueBox 2.x). Our
changes are purely additive, building on top of the JavaEE container
from JBoss.
from: http://markmail.org/message/zhjwhbgxarjsvdz7