Since I upgraded to the El Capitan beta (I'm now using the GM candidate) I can't get WebKit nightly to use its own engine: 1. There is no "Check for updates..." in the Safari menu. 2. It uses the built-in Safari 9 engine which can be easily verified by going to http://kangax.github.io/compat-table/es6/ and seeing how the results are identical to Safari 9, not WebKit ones. 3. If I open Safari, close it & then open WebKit I always get the popup with a message: "Your Safari extensions have been migrated.". Every single time. I haven't had such problems in earlier OS X releases. Reported originally at https://twitter.com/m_gol/status/639445068731035648.
The issue is "rootless" prevents DYLD env vars from being used. That is how we point Safari to the WebKit frameworks in the nightly bundle. We are working on a fix, but it will be via a Safari update not a nightly update.
Dropping WebKit nightlies from six-speed in light of this (all of my machines are now El Capitan). Will restore when the Safari fix lands.
*** Bug 150180 has been marked as a duplicate of this bug. ***
*** Bug 151212 has been marked as a duplicate of this bug. ***
https://trac.webkit.org/wiki/WebKitNightlyElCapWorkaround
This has been fixed in OS update that shipped a while ago.
It used to work and now the bug is back. :( I reported it again as bug 155786.