You could try the maven assembly plugin. I used it in conjunction with the appassembler plugin.
Configure appassembler to point to whatever name you want for your configuration directory, if you don't want 'etc'. The assembly plugin assembles everything in its own output directory, so I configure the assembly plugin to copy the bin and repo dirs from the appassembler directory into its output dir, then I have it copy the config files (mine are in src/main/config) into the expected config dir. There is some duplication in this, because you are copying the appassembler outputs, but that didn't really bother me.
So what you have after executing the assembly plugin is your bin, repo, and config dir are all peer directories under the assembly output directory. You can configure it to have a different structure if you prefer, I just wanted mine to mirror the appassembler structure.
The nice thing is that you can also configure the assembly plugin to change your binaries to executables, which I could't see how to do with appassembler. And, if you then bind appassembler:assemble and assembly:single goals to the package phase, all you have to do is 'mvn package', and it assembles everything.