With current hacks involving `org-agenda-files`, one cannot use org agenda
commands like clock in or change the entry's state to done, etc.
Specifically, the mangled behavior observed at #4901. This commit fixes those
problems around `org-agenda` buffer specific commands.
For more details, please refer to https://github.com/hlissner/doom-emacs/issues/4759#issuecomment-822100632.