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.