I am using minecraftforge-src-4.1.1.251, and a minecraft_server.jar straight from minecraft.net. Also mcp72. When I try to run install.sh, it says that the server jar is modified, but it isn't. When I go ahead anyway, it says this:

 

== MCP 7.2 (data: 7.2, client: 1.3.2, server: 1.3.2) ==
# found ff, ff patches, srgs, name csvs, doc csvs, param csvs, renumber csv, astyle, astyle config
> Creating Retroguard config files
== Decompiling client using fernflower ==
> Creating SRGs
> Applying Retroguard
> Compiling AccessTransformer
> Compiling MCPMerger
> Running MCPMerger
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 3, Size: 2
at java.util.ArrayList.add(ArrayList.java:367)
at cpw.mods.fml.common.asm.transformers.MCPMerger.processFields(MCPMerger.java:468)
at cpw.mods.fml.common.asm.transformers.MCPMerger.processClass(MCPMerger.java:384)
at cpw.mods.fml.common.asm.transformers.MCPMerger.processJar(MCPMerger.java:217)
at cpw.mods.fml.common.asm.transformers.MCPMerger.main(MCPMerger.java:107)
Decompile Exception: 1 

@TorchicBlaziken

 

You didn't mention your bin folder for minecraft.  You need to have a bin folder, which means you have to have a vanilla minecraft (without any mods, or forge), then I think you have to fire it up once, just to make it generate the bin folder.

 

Is it possible that's your problem?

 

Really, if you download mcp, forge, minecraft_server, and minecraft (client).  That should work perfectly.  I know it took me a few tries because I had so many modded .jars, I wound up just re-downloading everything new. :-)

Well, I had the bin folder and decompiling the client worked perfectly, it was only when it got to the server that things started going wrong.

If it says that the server or client is modified, then its modified, there is no other way around it.

Make sure you delete both your jars and the backups of the jars

And try agian.