I guess I'm not sure what's really missing here. I just went all the way through the following sample
and was able to do everything from eclipse - development, publish, test/run application client.
Basically, I right clicked on the app client project and did run as->java application. Alternatively, if i wanted to pass an argument in or set an environment variable ...I right clicked on the app client project and did run as->run confuigurations and it creates a new java application page in the run configuration dialog for me.
If more is needed than this, please provide details.