I was trying to run Charles.app on OS X 10.11 and had same issues as OP.

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You cannot develop android apps without java on a Mac, so this is a real bummer.

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But its a real PITA that well have to wait the mighty oracle to update JRE to have this sorted.

Im still rocking with Yosemite, so its good to be safe then sorry.

Applications or features that depend upon Java 6 may not function properly or will not launch when Java 6 is removed.

Developers should move to a newer version of Java as provided by Oracle.

The Oracle versions started when Apple stopped maintaining it.

Apple probably has to recompile it for 10.11, and do some testing.

For the first developer preview, it probably wasnt a huge concern to make sure it was done beforehand.

I dont recall if it was immediately available for previous DP1 releases.

Finally Its actually Oracles fault because heir installer does NOT configure Java 7, 8, or the pre-release 9 correctly.

On the internet you find a lot of people talking a lot of bull about this or similar issues.

But here I finally found: a) a good explanation of he issue b) an easy solution.

I did manage to add these folders with your solution and Im a little step closer to opening Flash Builder (4.6) on 10.11.

Also bear in mind that you have to change the terminal commands listed there to match your java version.