On El Capitan my Safari seems to have trouble remembering my settings for keychain: when the following pops up it stays there if I click "Allow" or "Always Allow". It goes away when I click "Deny" with the obvious consequence that the key is not used and my identification fails.

Is that a know bug? What can I do to diagnose it in more details or to fix it?

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Always Allow should add the application to the item's 'always allow' list. If it doesn't, you can try adding the application yourself.

  1. Open the keychain in Keychain Access.
  2. Find and open the 'Internet password' item for GitHub.
  3. In the Access Control tab, click the + and add Safari to the list.
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