allow etree.XMLParser to resolve external entities

We use XML external (file) entities to include .rst files for the help section in tool XMLs. U ntil recently this wasn't a problem, but the default in lxml was recently changed and there is no way in planemo linting or testing to set this flag for the XMLParser. 

This change mainly makes parse_xml() use the old default.

lib/galaxy/util/__init__.py

@@ -337,7 +337,7 @@ def parse_xml(
     if remove_comments and LXML_AVAILABLE:
         # If using stdlib etree comments are always removed,
         # but lxml doesn't do this by default
-        parser = etree.XMLParser(remove_comments=remove_comments)
+        parser = etree.XMLParser(remove_comments=remove_comments, resolve_entities=True)
 
     if LXML_AVAILABLE and schemafname:
         with open(str(schemafname), "rb") as schema_file: