• Module mod-hbm with bean class and .hbm.xml mapping for it.
• Module mod-cfg depends on mod-hbm.
• Module mod-cfg includes spring configuration with Hibernate factory bean.
• Spring configuration refers to resources from mod-hbm via mappingResources.
• Some .hbm.xml is added to mod-cfg just for example.
• Module mod-cfg has Web facet.

Make sure that the project is compiled, i.e. all xmls are copied to output.
Open project, check Java EE view. Hibernate factory is shown. Resources from mod-hbm are not included - that's another issue.
Now go to mod-cfg settings. Edit Web facet properties. Set "Copy output to" for mod-hbm. Ok.
Check Java EE view. It now has resources from mod-hbm too. Nice, but that's not all.
Select a BeanHbm.hbm.xml and Jump to source. Xml is opened. Check it's path (e.g. in tool tip). The file is from compiler's output!