--- commands.py
+++ commands.py
@@ -139,6 +139,8 @@
             fieldnames = csvreader.fieldnames
     return set(fieldnames)
 
+def commands_sanity_check():
+    print '    Commands patch applied successfully'
 
 class Commands(object):
     """Contains the commands and initialisation for a full mcp run"""
@@ -949,6 +951,8 @@
         binlk = {CLIENT: self.binclient, SERVER: self.binserver}
         testlk = {CLIENT: self.testclient, SERVER: self.testserver}
 
+        if side == SERVER and not os.path.exists(os.path.join(binlk[side], os.path.normpath(testlk[side] + '.class'))):
+            return self.checkbins(CLIENT)
         if not os.path.exists(os.path.join(binlk[side], os.path.normpath(testlk[side] + '.class'))):
             return False
         return True
@@ -1280,6 +1284,9 @@
         pathbinlk = {CLIENT: self.binclient, SERVER: self.binserver}
         pathsrclk = {CLIENT: self.srcclient, SERVER: self.srcserver}
         pathlog = {CLIENT: self.clientrecomplog, SERVER: self.serverrecomplog}
+        
+        if side == SERVER: #Warn about server because FML recombines it into client
+            self.logger.info('Server side recompiling might be skipped, this is normal, do not complain to FML/Forge team about server side.')
 
         if not os.path.exists(pathbinlk[side]):
             os.makedirs(pathbinlk[side])
@@ -1337,7 +1344,7 @@
             raise
 
     def startserver(self, mainclass, extraargs):
-        classpath = [self.binserver] + self.cpathserver
+        classpath = [self.binclient, self.srcclient] + self.cpathserver
         classpath = [os.path.join('..', p) for p in classpath]
         classpath = os.pathsep.join(classpath)
         os.chdir(self.dirjars)
@@ -1702,7 +1709,7 @@
         self.runcmd(forkcmd)
         return True
 
-    def gathermd5s(self, side, reobf=False):
+    def gathermd5s(self, side, reobf=False, skip_fml=False):
         if not reobf:
             md5lk = {CLIENT: self.md5client, SERVER: self.md5server}
         else:
@@ -1717,6 +1724,9 @@
                     class_path = ''
                 else:
                     class_path += '/'
+                if skip_fml:
+                    if class_path.startswith('cpw/'):
+                        continue
                 for class_file in fnmatch.filter(filelist, '*.class'):
                     class_name = class_path + os.path.splitext(class_file)[0]
                     bin_file = os.path.normpath(os.path.join(path, class_file))
@@ -1889,6 +1899,9 @@
                 sys.exit(1)
 
         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('Retrieving file from server : %s', entry[0])
                 cur_file = os.path.normpath(entry[0])
@@ -1909,6 +1922,9 @@
         md5reoblk = {CLIENT: self.md5reobfclient, SERVER: self.md5reobfserver}
         outpathlk = {CLIENT: self.srcmodclient, SERVER: self.srcmodserver}
         src = {CLIENT: self.srcclient, SERVER: self.srcserver}
+        
+        if side == SERVER: #Noop out server side stuff
+            return
 
         # HINT: We need a table for the old md5 and the new ones
         md5table = {}