On any resource, the properties dialog has a checkbox for read-only and a second check box labeled “Derived”. Here’s an excerpt from http://help.eclipse.org/help30/index.jsp?topic=/org.eclipse.platform.doc.isv/guide/resAdv_derived.htm explaining derived.
Many resources get created in the course of translating, compiling, copying, or otherwise processing files that the user creates and edits. Derived resources are resources that are not original data, and can be recreated from their source files. It is common for derived files to be excluded from certain kinds of processing.
It seems like derived resources would be good candidates for exclusion from auto-validation.
On the topic of timmytool’s original question, it seems renaming those merge files to use some extension other than .xml would solve his problem.