Change the mods and modListFile argument handling a bit. Other tweakers will get a chance at looking

at them now - they're only removed right before launch.

fml/src/main/java/cpw/mods/fml/common/launcher/FMLTweaker.java

@@ -130,6 +130,11 @@ public class FMLTweaker implements ITweaker {
     @Override
     public String getLaunchTarget()
     {
+        // Remove the extraneous mods and modListFile args
+        @SuppressWarnings("unchecked")
+        Map<String,String> args = (Map<String, String>) Launch.blackboard.get("launchArgs");
+        args.remove("--modListFile");
+        args.remove("--mods");
         return "net.minecraft.client.main.Main";
     }
 

fml/src/main/java/cpw/mods/fml/relauncher/ModListHelper.java

@@ -31,7 +31,6 @@ public class ModListHelper {
         if (listFile != null)
         {
             parseListFile(listFile);
-            args.remove("--modListFile");
         }
         String extraMods = args.get("--mods");
         if (extraMods != null)
@@ -41,7 +40,6 @@ public class ModListHelper {
             {
                 tryAddFile(modFile, null, modFile);
             }
-            args.remove("--mods");
         }
     }
     private static void parseListFile(String listFile) {
@@ -72,7 +70,7 @@ public class ModListHelper {
             FMLRelaunchLog.info("Failed to find the specified repository root %s", modList.repositoryRoot);
             return;
         }
-        
+
         for (String s : modList.modRef)
         {
             StringBuilder sb = new StringBuilder();
@@ -91,7 +89,7 @@ public class ModListHelper {
         }
     }
     private static void tryAddFile(String modFileName, File repoRoot, String descriptor) {
-        File modFile = repoRoot != null ? new File(repoRoot,modFileName) : new File(modFileName);  
+        File modFile = repoRoot != null ? new File(repoRoot,modFileName) : new File(modFileName);
         if (!modFile.exists())
         {
             FMLRelaunchLog.info("Failed to find mod file %s (%s)", descriptor, modFile.getAbsolutePath());