--- commands.py
+++ commands.py
@@ -584,6 +584,9 @@
         self.has_astyle_cfg = False
         if os.path.isfile(self.astyleconf):
             self.has_astyle_cfg = True
+            
+        #FML Entries
+        self.srcshared = os.path.normpath(os.path.join(self.dirsrc, 'common'))
 
     def creatergcfg(self, reobf=False, keep_lvt=False, keep_generics=False, rg_update=False):
         """Create the files necessary for RetroGuard"""
@@ -1198,20 +1201,20 @@
         with open(self.csvmethods, 'rb') as fh:
             methodsreader = csv.DictReader(fh)
             for row in methodsreader:
-                if int(row['side']) == side:
+                if int(row['side']) == side or int(row['side']) == 2:
                     if row['name'] != row['searge']:
                         names['methods'][row['searge']] = row['name']
         with open(self.csvfields, 'rb') as fh:
             fieldsreader = csv.DictReader(fh)
             for row in fieldsreader:
-                if int(row['side']) == side:
+                if int(row['side']) == side or int(row['side']) == 2:
                     if row['name'] != row['searge']:
                         names['fields'][row['searge']] = row['name']
         if self.has_param_csv:
             with open(self.csvparams, 'rb') as fh:
                 paramsreader = csv.DictReader(fh)
                 for row in paramsreader:
-                    if int(row['side']) == side:
+                    if int(row['side']) == side or int(row['side']) == 2:
                         names['params'][row['param']] = row['name']
 
         regexps = {
@@ -1309,6 +1312,11 @@
 
         # HINT: We pathwalk the sources
         for path, _, filelist in os.walk(pathsrclk[side], followlinks=True):
+            for cur_file in fnmatch.filter(filelist, '*.java'):
+                updatefile(os.path.normpath(os.path.join(path, cur_file)))
+                
+        # FML, copy of the above, for the common folder
+        for path, _, filelist in os.walk(self.srcshared, followlinks=True):
             for cur_file in fnmatch.filter(filelist, '*.java'):
                 updatefile(os.path.normpath(os.path.join(path, cur_file)))
         return True
@@ -1442,6 +1450,21 @@
         if not self.has_astyle_cfg:
             self.logger.warning('!! reformatting disabled due to no config !!')
             return False
+            
+        #FML Recall this function on the common folder
+        #Potential bug: If this is called without a subsiquent rename call, will cause double comments
+        if pathsrclk[side] != self.srcshared:
+            if side == CLIENT:
+                tmp = self.srcclient
+                self.srcclient = self.srcshared
+                self.process_javadoc(side)
+                self.srcclient = tmp
+            else:
+                tmp = self.srcserver
+                self.srcserver = self.srcshared
+                self.process_javadoc(side)
+                self.srcserver = tmp
+                
 
         # HINT: We create the list of source directories based on the list of packages
         pkglist = filterdirs(pathsrclk[side], '*.java', append_pattern=True)
@@ -1591,6 +1614,9 @@
             return
 
         for entry in newfiles:
+            if 'commands.py' in entry[0]: #FML, Disable updating of Commands.py
+                print 'Update to runtime/commands.py found, but disbled due to using fml'
+                continue
             if entry[3] == 'U':
                 self.logger.info('New version found for : %s', entry[0])
             elif entry[3] == 'D':