--- commands.py
+++ commands.py
@@ -58,6 +58,8 @@
 
 
 def reallyrmtree(path):
+    if os.path.isfile(os.path.join(path, 'asm-all-4.0.jar')): #Check if asm exists, indicating the libs folder, if so, don't delete it
+        return
     if not sys.platform.startswith('win'):
         if os.path.exists(path):
             shutil.rmtree(path)
@@ -788,6 +790,8 @@
         binlk = {CLIENT: self.binclient, SERVER: self.binserver}
         testlk = {CLIENT: self.testclient, SERVER: self.testserver}
 
+        if side == SERVER:
+            return self.checkbins(CLIENT)
         if not os.path.exists(os.path.join(binlk[side], os.path.normpath(testlk[side] + '.class'))):
             return False
         return True
@@ -1062,7 +1066,7 @@
             raise
 
     def startserver(self):
-        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)
@@ -1070,7 +1074,7 @@
         self.runmc(forkcmd)
 
     def startclient(self):
-        classpath = [self.binclient] + self.cpathclient
+        classpath = [self.binclient, self.srcclient] + self.cpathclient
         classpath = [os.path.join('..', p) for p in classpath]
         classpath = os.pathsep.join(classpath)
         natives = os.path.join('..', self.dirnatives)
@@ -1197,20 +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 = {
@@ -1344,13 +1348,13 @@
         methods = {}
         for row in methodsreader:
             #HINT: Only include methods that have a non-empty description
-            if int(row['side']) == side and row['desc']:
+            if (int(row['side']) == side or int(row['side']) == 2) and row['desc']:
                 methods[row['searge']] = row['desc'].replace('*/', '* /')
 
         fields = {}
         for row in fieldsreader:
             #HINT: Only include fields that have a non-empty description
-            if int(row['side']) == side and row['desc']:
+            if (int(row['side']) == side or int(row['side']) == 2) and row['desc']:
                 fields[row['searge']] = row['desc'].replace('*/', '* /')
 
         regexps = {
@@ -1427,7 +1431,7 @@
         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:
@@ -1442,6 +1446,9 @@
                     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))
@@ -1535,6 +1542,8 @@
         if not os.path.exists(outpathlk[side]):
             os.makedirs(outpathlk[side])
 
+        reserved = ['CON', 'PRN', 'AUX', 'NUL', 'COM1', 'COM2', 'COM3', 'COM4', 'COM5', 'COM6', 'COM7', 'COM8', 'COM9', 'LPT1', 'LPT2', 'LPT3', 'LPT4', 'LPT5', 'LPT6', 'LPT7', 'LPT8', 'LPT9']
+
         # HINT: We extract the modified class files
         with closing(zipfile.ZipFile(jarlk[side])) as zipjar:
             for in_class in trgclasses:
@@ -1548,6 +1557,23 @@
                     out_class = out_class.replace(self.nullpkg, '')
                     if out_class[0] == '/':
                         out_class = out_class[1:]
+                        
+                rename = False
+                for res in reserved:
+                    if out_class.upper().startswith(res):
+                        rename = True
+                        break
+                        
+                if rename:
+                    try:
+                        f = open(os.path.join(outpathlk[side], '_' + out_class), 'wb')
+                        f.write(zipjar.read(out_class))
+                        f.close()
+                        self.logger.info('> Outputted %s to %s as %s', in_class.ljust(35), outpathlk[side], '_' + out_class)
+                    except IOError:
+                        self.logger.error('* File %s failed extracting for %s', out_class, in_class)
+                    continue
+                
                 try:
                     zipjar.extract(out_class, outpathlk[side])
                     self.logger.info('> Outputted %s to %s as %s', in_class.ljust(35), outpathlk[side], out_class)
@@ -1594,6 +1620,9 @@
                 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])
@@ -1614,6 +1643,9 @@
         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 = {}
@@ -1656,3 +1688,6 @@
                 except IOError:
                     self.logger.error('* File %s copy failed', in_class)
 
+def commands_sanity_check():
+    print 'Commands patch applied successfully'
+