When I upgraded to El Capitan, I ran into 2 issues with Adobe DreamWeaver CS6.
1) It didn't start and needed Java ... not sure where that went.
2) After I installed Java (tried Apple's 2015-001 version and Oracles latest version JDK) DreamWeaver didn't work properly.
With "didn't work properly" I mean: I could not select items or text properly. It acted really weird and became totally useless to me.
Finally I just copied the content of a previous Mac OS X (10.10) version over to the El Capitan Mac and ... both problems resolved instantly.
OK, so first of all - this is probably not the "cleanest" way to do this, but it worked for me ... and you're doing this at your own risk!
On the Mac that runs OS 10.10 (for example) copy the entire /Library/Java directory to a USB stick.
Next step is to copy these files to your El Capitan setup, overwriting the existing files. But this comes with the "rootless" problem. Even as root you're allowed to overwrite these directories. In Terminal execute the following an restart your El Capitan Mac:
sudo nvram boot-args="rootless=0"
Now copy the files from the USB stick overwriting the original files. Finder and Path Finder didn't help me with that so I had to do this in terminal again:
rm -rf /Libraries/Java
cp -r /Volumes/<your USB stick>/Java /Library/
Once done, we better re-enable rootless mode with:
sudo nvram boot-args="rootless=1"
and reboot your El Capitan Mac again.
Try DreamWeaver now ... and in my case: everything worked as it used to do.
Thanks Apple for breaking something, thanks Adobe for going CC on us.