Simply using "extends DefaultWebProject(info) with PrecompilerWebProject" on my SBT project was leading to irregular results, where the output template .class files would usually not get into my .war, but sometimes would, especially after I touched a .scala file and re-published. Generally, the .class files would get built, but then the prepare-webapp step would delete them.

The fine folks on #scalatra channel suggested this line in my Project:

  override def precompileTemplatesAction = super.precompileTemplatesAction dependsOn prepareWebapp

This seems to successfully order the PCT step after the prepare-webapp step, and my builds have been working since.

casualjim also suggested override def runAction = task { args => super.runAction(args) dependsOn(precompileTemplatesAction) }, which I did not try.