Or, instead of the DEVONthink Clipper icon, in Safari press the Share icon and select “Add to DEVONthink” – this opens the Clipper without the message. Click here or click there – still just one click.
FYI, if you want to use a keyboard shortcut for this, go to System Preferences -> Keyboard -> Shortcuts -> App Shortcuts -> Click the Plus button at the bottom -> Make sure All Applications is selected in the Dropdown menu then add ‘File->Share->Add to DEVONthink’ (without the quotes) in the menu title box. Then select a keyboard shortcut and it will automatically bring up the dialog box in most applications (including Safari).
I guess this is an old thread, so I’m not sure how useful this comment will be. But it does seem worth mentioning.
I’m using using macOS 10.14.5.
When I’m running Safari 12.1.1, and I try to access Clip to Devonthink 1.0 (for DevonThink 3.0) by clicking the icon in Safari, I am asked if I want to allow this page to open DevonThink 3.0.
Of course, I don’t like this. It adds an extra click every time I want to do this.
But I still have installed the Clip to Devonthink 1.2.6 for the previous version of DevonThink. When I use this, I do not get the annoying pop up message, and everything works fine. I can actually use the old Clip to DevonThink to clip to DevonThink 3.0.
This is a bit odd, I think. But there does seem to be something that Clip to Devonthink 1.2.6 does better than the new version.
You should not have both extensions installed.
Also, the 1.2.6 is the one that will initiate the prompt from Safari.
The 1.0 extension is a native Safari extension that doesn’t require extra intervention.