Sanitize input to isRemappedClass to use '/' as a package seperator like the srg files.

common/cpw/mods/fml/common/asm/transformers/deobf/FMLDeobfuscatingRemapper.java

@@ -125,6 +125,7 @@ public class FMLDeobfuscatingRemapper extends Remapper {
 
     public boolean isRemappedClass(String className)
     {
+        className = className.replace('.', '/');
         return classNameBiMap.containsKey(className) || mcpNameBiMap.containsKey(className) || (!classNameBiMap.isEmpty() && className.indexOf('/') == -1);
     }