diff --git a/fml/.gitignore b/fml/.gitignore
index c5a46eb4c4..6c6c3b08e4 100644
--- a/fml/.gitignore
+++ b/fml/.gitignore
@@ -9,3 +9,4 @@
 /target
 fmlbranding.properties
 /fernflower.zip
+/commands.py.bck
diff --git a/fml/build.xml b/fml/build.xml
index e07b5c8afc..c6222bb000 100644
--- a/fml/build.xml
+++ b/fml/build.xml
@@ -307,7 +307,7 @@
     <exec executable="${python.exe}" dir="${basedir}">
       <arg value="${basedir}/update_patches.py" />
       <arg value="${mcp.home}"/>
-      <arg value="${patch.src.dir}"/>
+      <arg value="${basedir}"/>
     </exec>
   </target>
 
diff --git a/fml/commands.patch b/fml/commands.patch
new file mode 100644
index 0000000000..8197d8ac23
--- /dev/null
+++ b/fml/commands.patch
@@ -0,0 +1,93 @@
+--- commands.py
++++ commands.py
+@@ -22,6 +22,7 @@
+ import errno
+ import shlex
+ import platform
++import pprint
+ from hashlib import md5  # pylint: disable-msg=E0611
+ from contextlib import closing
+ from textwrap import TextWrapper
+@@ -502,6 +503,7 @@
+         self.binclienttmp = os.path.normpath(config.get('OUTPUT', 'BinClientTemp'))
+         self.binservertmp = os.path.normpath(config.get('OUTPUT', 'BinServerTemp'))
+         self.srcclient = os.path.normpath(config.get('OUTPUT', 'SrcClient'))
++        self.srcshared = os.path.normpath(os.path.join(self.dirsrc, 'common'))
+         self.srcserver = os.path.normpath(config.get('OUTPUT', 'SrcServer'))
+         self.testclient = config.get('OUTPUT', 'TestClient')
+         self.testserver = config.get('OUTPUT', 'TestServer')
+@@ -1039,6 +1041,7 @@
+             all_files = True
+             append_pattern = False
+         pkglist = filterdirs(pathsrclk[side], '*.java', append_pattern=append_pattern, all_files=all_files)
++        pkglist = pkglist + filterdirs(self.srcshared, '*.java', append_pattern=True) #FML, Add Common folder
+         dirs = ' '.join(pkglist)
+         classpath = os.pathsep.join(cplk[side])
+         forkcmd = self.cmdrecomp.format(classpath=classpath, sourcepath=pathsrclk[side], outpath=pathbinlk[side],
+@@ -1238,6 +1241,11 @@
+ 
+         # 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
+@@ -1320,12 +1328,14 @@
+         pathsrclk = {CLIENT: self.srcclient, SERVER: self.srcserver}
+ 
+         strip_comments(pathsrclk[side])
++        strip_comments(self.srcshared)
+ 
+     def process_cleanup(self, side):
+         """Do lots of random cleanups including stripping comments, trailing whitespace and extra blank lines"""
+         pathsrclk = {CLIENT: self.srcclient, SERVER: self.srcserver}
+ 
+         src_cleanup(pathsrclk[side], fix_imports=True, fix_unicode=True, fix_charval=True, fix_pi=True, fix_round=False)
++        src_cleanup(self.srcshared, fix_imports=True, fix_unicode=True, fix_charval=True, fix_pi=True, fix_round=False)
+ 
+     def process_javadoc(self, side):
+         """Add CSV descriptions to methods and fields as javadoc"""
+@@ -1334,6 +1344,21 @@
+         if not self.has_doc_csv:
+             self.logger.warning('!! javadoc disabled due to no csvs !!')
+             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
++                process_javadoc(self, side)
++                self.srcclient = tmp
++            else:
++                tmp = self.srcserver
++                self.srcserver = self.srcshared
++                process_javadoc(self, side)
++                self.srcserver = tmp
++                
+ 
+         #HINT: We read the relevant CSVs
+         methodsreader = csv.DictReader(open(self.csvmethods, 'r'))
+@@ -1420,6 +1445,7 @@
+ 
+         # HINT: We create the list of source directories based on the list of packages
+         pkglist = filterdirs(pathsrclk[side], '*.java', append_pattern=True)
++        pkglist = pkglist + filterdirs(self.srcshared, '*.java', append_pattern=True) #FML, Add Common folder
+         dirs = ' '.join(pkglist)
+         forkcmd = self.cmdastyle.format(classes=dirs, conffile=self.astyleconf)
+         self.runcmd(forkcmd)
+@@ -1592,6 +1618,9 @@
+                 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])
diff --git a/fml/decompile.py b/fml/decompile.py
index 3a4ab6f64a..435718f4fd 100644
--- a/fml/decompile.py
+++ b/fml/decompile.py
@@ -13,6 +13,7 @@ if __name__ == '__main__':
         
         sys.path.append(os.path.join(fml_dir, 'install'))
         
-        from fml import setup_fml
+        from fml import setup_fml, setup_mcp
         
+        setup_mcp(fml_dir, mcp_dir)
         setup_fml(fml_dir, mcp_dir)
diff --git a/fml/install/fml.py b/fml/install/fml.py
index 877fea18c7..51a03c17f0 100644
--- a/fml/install/fml.py
+++ b/fml/install/fml.py
@@ -1,7 +1,7 @@
 import os, os.path, sys
 import urllib, zipfile
 import shutil, glob, fnmatch
-import subprocess, logging, re
+import subprocess, logging, re, shlex
 from hashlib import md5  # pylint: disable-msg=E0611
 
 #class flushout(object):
@@ -157,7 +157,7 @@ def setup_fml(fml_dir, mcp_dir):
             
         #Compile AccessTransformer
         forkcmd = ('%s -Xlint:-options -deprecation -g -source 1.6 -target 1.6 -classpath "{classpath}" -sourcepath {sourcepath} -d {outpath} {target}' % self.cmdjavac).format(
-            classpath=os.path.join(mcp_dir, 'lib', '*'), sourcepath=os.path.join(fml_dir, 'common'), outpath=os.path.join(fml_dir, 'bin'), 
+            classpath=os.pathsep.join(['.', os.path.join(mcp_dir, 'lib', '*')]), sourcepath=os.path.join(fml_dir, 'common'), outpath=os.path.join(fml_dir, 'bin'), 
             target=os.path.join(fml_dir, 'transformers', 'cpw', 'mods', 'fml', 'common', 'asm', 'transformers', 'AccessTransformer.java'))
         print forkcmd
         self.runcmd(forkcmd)
@@ -429,3 +429,42 @@ def merge_tree(root_src_dir, root_dst_dir):
             if os.path.exists(dst_file):
                 os.remove(dst_file)
             shutil.copy(src_file, dst_dir)
+            
+def setup_mcp(fml_dir, mcp_dir):
+    backup = os.path.join(fml_dir, 'commands.py.bck')
+    runtime = os.path.join(mcp_dir, 'runtime', 'commands.py')
+    patch = os.path.join(fml_dir, 'commands.patch')
+    
+    print 'Setting up MCP'
+    if os.path.isfile(backup):
+        print '> Restoring commands.py backup'
+        if os.path.exists(runtime):
+            os.remove(runtime)
+        shutil.copy(backup, runtime)
+    else:
+        print '> Backing up commands.py'
+        shutil.copy(runtime, backup)
+    
+    if not os.path.isfile(patch):
+        return
+        
+    temp = os.path.abspath('temp.patch')
+    cmd = 'patch -i "%s" ' % temp
+    
+    windows = os.name == 'nt'
+    if windows:
+        applydiff = os.path.abspath(os.path.join(mcp_dir, 'runtime', 'bin', 'applydiff.exe'))
+        cmd = '"%s" -uf -i "%s"' % (applydiff, temp)
+        
+    if os.sep == '\\':
+        cmd = cmd.replace('\\', '\\\\')
+    cmd = shlex.split(cmd)
+    
+    if windows:
+        print 'Patching file %s' % os.path.normpath(runtime)
+    fix_patch(patch, temp)
+    process = subprocess.Popen(cmd, cwd=os.path.join(mcp_dir, 'runtime'), bufsize=-1)
+    process.communicate()
+
+    if os.path.isfile(temp):
+        os.remove(temp)
\ No newline at end of file
diff --git a/fml/install/install.py b/fml/install/install.py
index 5170dbc059..6b4ca83bca 100644
--- a/fml/install/install.py
+++ b/fml/install/install.py
@@ -3,10 +3,11 @@ import os, os.path, sys
 fml_dir = os.path.dirname(os.path.abspath(__file__))
 mcp_dir = os.path.abspath('..')
 
-from fml import setup_fml, finish_setup_fml, apply_fml_patches
+from fml import setup_fml, finish_setup_fml, apply_fml_patches, setup_mcp
 
 def main():
     print '================ Forge ModLoader Setup Start ==================='
+    setup_mcp(fml_dir, mcp_dir)
     setup_fml(fml_dir, mcp_dir)
     apply_fml_patches(fml_dir, mcp_sir, os.path.join(mcp_dir, 'src'))
     finish_setup_fml(fml_dir, mcp_dir)
diff --git a/fml/update_patches.py b/fml/update_patches.py
index f012215f84..f1fe703de1 100644
--- a/fml/update_patches.py
+++ b/fml/update_patches.py
@@ -3,7 +3,7 @@ import os
 import commands
 import fnmatch
 import re
-import subprocess, shlex
+import subprocess, shlex, shutil
 
 import difflib, time
 
@@ -30,7 +30,8 @@ def cleanDirs(path):
 def main():
     print("Creating patches")
     mcp = os.path.normpath(sys.argv[1])
-    patchd = os.path.normpath(sys.argv[2])
+    fml_dir = os.path.normpath(sys.argv[2])
+    patchd = os.path.normpath(os.path.join(fml_dir, 'patches'))
     base = os.path.normpath(os.path.join(mcp, 'src-base'))
     work = os.path.normpath(os.path.join(mcp, 'src-work'))
     
@@ -62,5 +63,24 @@ def main():
 
     cleanDirs(patchd)
     
+    backup = os.path.join(fml_dir, 'commands.py.bck')
+    runtime = os.path.join(mcp, 'runtime', 'commands.py')
+    patch_file = os.path.join(fml_dir, 'commands.patch')
+    
+    if not os.path.exists(backup):
+        shutil.copy(runtime, backup)
+    
+    patch = ''.join(difflib.unified_diff(open(backup, 'U').readlines(), open(runtime, 'U').readlines(), 'commands.py', 'commands.py', '', '', n=3))
+    if len(patch) > 0:
+        print 'Creating commands.py patch'
+        patch = patch.replace('\r\n', '\n')
+        
+        with open(patch_file, 'wb') as fh:
+            fh.write(patch)
+    else:
+        if os.path.isfile(patch_file):
+            print("Deleting empty commands.py patch")
+            os.remove(patch_file)
+    
 if __name__ == '__main__':
     main()