In looking at the stack trace this is coming from the Java refactoring module.  The "getSourceGroup" method needs to tolerate being called on project types 
where it doesn't find java sources.  (I fixed something similar in the Ruby copy myself.)

(I don't think this is I18N related)

Here's the Java implementation:

    static SourceGroup getSourceGroup(FileObject file) {
        Project prj = FileOwnerQuery.getOwner(file);
        if (prj == null)
            return null;
        Sources src = ProjectUtils.getSources(prj);
        //TODO: needs to be generified
        SourceGroup[] javagroups = src.getSourceGroups(JavaProjectConstants.SOURCES_TYPE_JAVA);
        SourceGroup[] xmlgroups = src.getSourceGroups("xml");//NOI18N

        SourceGroup[] allgroups =  new SourceGroup[javagroups.length + xmlgroups.length];
        System.arraycopy(javagroups,0,allgroups,0,javagroups.length);
        System.arraycopy(xmlgroups,0,allgroups,allgroups.length-1,xmlgroups.length);
        for(int i=0; i<allgroups.length; i++) {
            if (allgroups[i].getRootFolder().equals(file) || FileUtil.isParentOf(allgroups[i].getRootFolder(), file))
                return allgroups[i];
        }
        return null;
    }


Here's what I now have for Ruby:

    static SourceGroup getSourceGroup(FileObject file) {
        Project prj = FileOwnerQuery.getOwner(file);
        if (prj == null)
            return null;
        Sources src = ProjectUtils.getSources(prj);
        //TODO: needs to be generified
        SourceGroup[] rubygroups = src.getSourceGroups(RubyProject.SOURCES_TYPE_RUBY);
        SourceGroup[] xmlgroups = src.getSourceGroups("xml");//NOI18N

        if (rubygroups.length == 0 && xmlgroups.length == 0) {
            // Probably used as part of some non-Ruby-related project refactoring operation (#106987)
            return null;
       }

        SourceGroup[] allgroups =  new SourceGroup[rubygroups.length + xmlgroups.length];
        System.arraycopy(rubygroups,0,allgroups,0,rubygroups.length);
        System.arraycopy(xmlgroups,0,allgroups,allgroups.length-1,xmlgroups.length);
        for(int i=0; i<allgroups.length; i++) {
            if (allgroups[i].getRootFolder().equals(file) || FileUtil.isParentOf(allgroups[i].getRootFolder(), file))
                return allgroups[i];
        }
        return null;
    }

Checking in FolderTreeElement.java;
/cvs/refactoring/java/src/org/netbeans/modules/refactoring/java/ui/tree/FolderTreeElement.java,v  <-- 
FolderTreeElement.java
new revision: 1.6; previous revision: 1.5
done

I improved logging. There should be no exception thrown, but there should be error message in the console:
Cannot find SourceGroup for /some/file

And I like to know which file is the bad one.
Thanks

Marking as fixed. Please reopen if it happens again

v.