This might possibly need to be the highest priority.
Same thing happens on a fresh Ubuntu GNOME zesty installation (see the
attachment).
I thought that installing a new one might be a good workaround, so I
went to extensions.gnome.org, picked a random extension, and installed
it.
Nope, even though it's installed, it's not turned on and I still can't
touch a thing in that window.
After that, I've tried enabling them using:
gnome-shell-extension-tool -e <EXTENSION_NAME>
As the output, I get a message saying that the extension has been
enabled, which is not the case. Restarting the GNOME Shell also didn't
work.
...and only at this point, I've noticed the global setting for enabling
the extensions, which indeed re-enables all of them.
** Attachment added: "Screenshot from 2017-04-14 12-49-11.png"
https://bugs.launchpad.net/ubuntu/+source/gnome-tweak-tool/+bug/1681918/+attachment/4861962/+files/Screenshot%20from%202017-04-14%2012-49-11.png
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https://bugs.launchpad.net/bugs/1681918
Title:
GNOME Tweak Tool disables all extensions when removing one extension
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