jACT-R did support command line execution back in the day. It was meant to make it easier to execute in "lighter" environments (i.e., within a game engine, controlling a robot, on a cell phone, whatever). As time progressed, it became clear that a general solution for that was at odds with the primary use case: modelers trying to build and analyze their particular phenomenon.
The primary use case relies heavily upon OSGi and Eclipse's dynamic and modular tools. These, however, make traditional command lines much more difficult (and unwieldy). OSGi and Eclipse dynamically check project dependencies and securely set up the various classloaders and resource paths, as well as extensions (for parser, compilers, modules, extensions, etc.) and the actual runtime environment.
This does not mean that you can't run from the command line. You can, but it is a really bad idea to use that mode for the development of a model. Only after you have built, tested, and hardened your model in the IDE should you even think about embedding or command line execution.
Let's assume your model is the awesomsauce and you want to run it command line now. First, you will need the environment.xml file that the IDE generated in the run directory. This tells the org.jactr.entry.Main entry point how to assemble the environment. You will want to strip out the attachments : org.jactr.tools.async.controller.RemoteInterface and org.jactr.tools.tracer.RuntimeTracer, as they are only for IDE runs.
Next, you need the command line that Eclipse uses. To do this, run your model, switch to the debug view and bring up the properties of the running processes. It will include the actual command line. It looks something like this:
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java -Dorg.apache.commons.logging.log=org.apache.commons.logging.impl.Log4JLogger -Dlog4j.configuration=file:/Users/harrison/Archive/Development/workspaces/modeling-dev/mil.navy.nrl.ncarai.associative.fan/jactr-log.xml -Dfile.encoding=MacRoman -Xbootclasspath/p:/Users/harrison/Archive/Development/Apps/3.7/eclipse-model-dev-32/plugins/org.eclipse.jdt.debug_3.7.100.v20120529-1702/jdi.jar -classpath /Users/harrison/Archive/Development/Apps/3.7/eclipse-model-dev-32/plugins/org.eclipse.equinox.launcher_1.3.0.v20120522-1813.jar org.eclipse.equinox.launcher.Main -application org.jactr.launching.application -data /Users/harrison/.jactr/workspaces/mil.navy.nrl.ncarai.associative.fan -configuration file:/Users/harrison/.jactr/configuration/mil.navy.nrl.ncarai.associative.fan/Embodied-Fan-actual/ -dev file:/Users/harrison/.jactr/configuration/mil.navy.nrl.ncarai.associative.fan/Embodied-Fan-actual/dev.properties -name jACTR -nosplash -os macosx -arch x86 -e file:/Users/harrison/Archive/Development/workspaces/modeling-dev/mil.navy.nrl.ncarai.associative.fan/runs/8.16.12/9.49.28AM/environment.xml
There's a lot of mess in there. Let's break it down.
That will get you up and running on the command line, but again, I don't recommend it. The IDE provides you a ton of tools that will help you understand your model. Command line ninjas will always be at a disadvantage here.