modify whitespace replace fn directly

src/packages/whitespace/lib/whitespace.coffee

@@ -4,14 +4,18 @@ module.exports =
 
   configDefaults:
     ensureSingleTrailingNewline: true
-    ignoredGrammars: ["GitHub Markdown"]
 
   whitespaceBeforeSave: (editSession) ->
     buffer = editSession.buffer
     buffer.on 'will-be-saved', ->
-      return if editSession.getGrammar().name in config.get("whitespace.ignoredGrammars")
       buffer.transact ->
-        buffer.scan /[ \t]+$/g, ({replace}) -> replace('')
+        regex = null
+
+        buffer.scan /[ \t]+$/g, ({match, replace}) -> 
+          # GFM permits two whitespaces at the end of a line--trim anything else
+          unless editSession.getGrammar().scopeName = "scope.gfm" and match[0].length == 2
+            replace('')
+
         if config.get('whitespace.ensureSingleTrailingNewline')
           if buffer.getLastLine() is ''
             row = buffer.getLastRow() - 1