Hello,
I've exactly same problem, but even i put my source in src/common folder and when reobfuscate prompt says:
== MCP 7.25 (data: 7.25, client: 1.4.6, server: 1.4.6) ==
# found ff, ff patches, srgs, name csvs, doc csvs, param csvs, renumber csv, ast
yle, astyle config
> Creating Retroguard config files
== Reobfuscating client ==
> Cleaning reobf
> Generating md5s
> Packing jar
> Reobfuscating jar
> Extracting modified classes
> Modified class found : xxxxxxx/yyyyyyyyy
> Modified class found : xxxxxxx/zzzzzzzzzz
> Outputted xxxxxxx/yyyyyyyyy to reobf\minecraft as xxxxxxx/yyyyyyyyy.class
> Outputted xxxxxxx/zzzzzzzzzz to reobf\minecraft as xxxxxxx/zzzzzzzzzzi.class
- Done in 83.33 seconds
== Reobfuscating server ==
> Cleaning reobf
> Generating md5s
> Packing jar
> Reobfuscating jar
> Extracting modified classes
- Done in 39.66 seconds
in fact reobfuscated only two classes, but I've many more in my mod. why? please help.