Something like this: (copied from Cuyahoga build file)
Code:
<csc target="library" output="${build.dir}/bin/Cuyahoga.Core.dll" debug="${build.debug}"
         doc="${build.dir}/bin/Cuyahoga.Core.xml">
   <sources>
      <include name="Core/**/*.cs" />
   </sources>
   <resources dynamicprefix="true" prefix="Cuyahoga">
      <include name="Core/Domain/*.hbm.xml" />
   </resources>
   <references>
      <include name="System.dll" />
 ...
   </references>
</csc>
You might have to tweak the prefixes a little to make sure that the resource names match the namespaces of the domain classes.