Some more fixes to the ant stuff: apply patches now happens at the right time, I grab fernflower as part of

setup and added an updatepatches call too

fml/build.xml

@@ -220,6 +220,10 @@
     </condition>
     <fail if="do.not.continue">You have decided not to continue. This script will stop now.</fail>
     <echo>Preparing the MCP environment at ${mcp.home}</echo>
+    <exec executable="${python.exe}" dir="${basedir}">
+      <arg value="${basedir}/download_fernflower.py" />
+      <arg value="${mcp.home}"/>
+    </exec>
     <exec executable="${python.exe}" dir="${mcp.home}">
       <arg value="${mcp.home}/runtime/cleanup.py" />
       <arg value="-f" />
@@ -244,13 +248,20 @@
     <copy todir="${mcp.home}/src-base">
       <fileset dir="${mcp.home}/src"/>
     </copy>
-    <echo>Creating clean patch references at ${mcp.home}/src-work</echo>
+    <antcall target="patch"/>
+    <echo>Creating clean patched references at ${mcp.home}/src-work</echo>
     <copy todir="${mcp.home}/src-work">
       <fileset dir="${mcp.home}/src"/>
     </copy>
-    <antcall target="patch"/>
     <antcall target="writeversion"/>
     <echo>Setup complete! You should now be able to open ${basedir}/eclipse as a workspace in eclipse and import/refresh the FML-Server and FML-Client projects</echo>
   </target>
 
+  <target name="updatepatches" depends="buildenvsetup">
+    <exec executable="${python.exe}" dir="${basedir}">
+      <arg value="${basedir}/update_patches.py" />
+      <arg value="${mcp.home}"/>
+      <arg value="${basedir}/patches"/>
+    </exec>
+  </target>
 </project>

fml/download_fernflower.py

@@ -1,10 +1,17 @@
 import urllib
 import zipfile
+import sys
+import os
 
 if __name__ == '__main__':
     try:
         urllib.urlretrieve("http://goo.gl/PnJHp", './fernflower.zip')
+        if len(sys.argv)>1:
+          path = os.path.abspath(os.path.join(sys.argv[1],'runtime/bin'))
+        else:
+          path = os.path.abspath('../runtime/bin')
         zf = zipfile.ZipFile('fernflower.zip')
-        zf.extract('fernflower.jar', '../runtime/bin')
+        zf.extract('fernflower.jar', path)
+        print "Fernflower downloaded into MCP at %s" % (path)
     except:
-        print "Downloading Fernflower failed download manually from http://goo.gl/PnJHp"
+        print "Downloading Fernflower failed download manually from http://goo.gl/PnJHp"

fml/update_patches.py

@@ -27,10 +27,11 @@ def cleanDirs(path):
         
 def main():
     print("Creating patches")
-    mcp = sys.argv[1]    
+    mcp = sys.argv[1]
     base = os.path.normpath(os.path.join(mcp, 'src-base'))
     work = os.path.normpath(os.path.join(mcp, 'src-work'))
     timestamp = re.compile(r'[0-9-]* [0-9:\.]* [+-][0-9]*\r?\n')
+    mcpath = re.compile(mcp)
     
     for path, _, filelist in os.walk(work, followlinks=True):
         for cur_file in fnmatch.filter(filelist, '*.java'):
@@ -46,6 +47,7 @@ def main():
             if len(patch) > 0:
                 print patch_file
                 patch = timestamp.sub("0000-00-00 00:00:00.000000000 -0000\n", patch)
+                patch = mcpath.sub('..',patch)
                 patch = patch.replace('\r\n', '\n')
                 
                 if not os.path.exists(patch_dir):