1. It is very important to install SOA Software and JDeveloper in totally different Middleware Homes (means different folders).
2. Looks like you already upgraded your WLS + SOA to 11.6 and ofcourse RCU Database also.
3. When you download and install JDeveloper 11.6, in first screen, by default it will select above middleware home and will ask you, if this is where you want to install JDeveloper. Make sure you do NOT select this location where you have WLS + SOA. Instead select like create new middleware home and say on Windows give a path like C:\Oracle\Middleware\JDeveloper116 and this folder will have JDeveloper. Usually for WLS + SOA, I install to a folder like C:\Oracle\MiddlewareSOA115 etc.
If you install both in same middleware home, some jars gets overwritten and you run into wierd issues.
When you install JDeveloper, it should NOT even look for any SOA Software or version etc. JDeveloper is just the IDE. Install JDeveloper. From Help menu, you install 2 extensions for soa and bpm. Thats it.
I hope ORACLE documentation clearly states that the middleware homes should be different for JDev and WLS or atleast this is Recommended or Supported. If it already does, pardon me.
"You can create a new Middleware Home directory, or select one from a list of existing Middleware Home directories. If you choose a directory that already has Oracle JDeveloper and Oracle WebLogic Server components installed on it, you are taken directly to the Choose Products and Components screen to select additional components to install."
But a note 2 pharagraphs down says:
"The JDeveloper component should always be installed in new Middleware Home. The only component in the Oracle installer that can be installed into an existing Middleware Home is the Application Development Framework, and that should not be done if ADF has already been installed on the system by other Oracle Fusion Middleware products."
I will follow your suggestion and I'll post the results soon.
Thanks for Sharing this addition information (Section 3.3) which I never saw earlier. This section totally makes sense. This clearly means if you have WLS + SOA, your JDeveloper should have a different new middleware home. BUT if you just have WLS or WLS+ADF, then you can install JDeveloper also on this same middleware home.
One thing, when we install JDeveloper, it comes with basic Integrated Weblogic Server (light weight weblogic server) and also one default Ready to use DefaultDomain. Now on this DefaultDomain, we can pretty much deploy and test any standard J2EE application like EJBs, WebApps, WebServices, ADF Applications etc etc EXCEPT for SOA/ BPM applications. To deploy soa/bpm we do need a separate wls+soa env. It is also not recommended to deploy SOA on existing middleware where you already have JDevleoper.
End of the day, JDevloper and WLS+SOA should be in different folders, to make everybody's like happy :).