Aquamacs is a version of GNU Emacs configured to behave in a more OSX way like TextEdit. This means that each thing is in a separate OS Window. Later versions of Aquamacs and macOS have added tabs so things can open in a new tab.
Thus Aquamacs is behaving as designed.
You can limit the number of new OS Windows/Emacs frames that are opened by customising ...
Customize default-frame-list to have values for frame parameters top and left that put it in the middle of your screen. (Use M-x customize-option default-frame-alist.)
If that doesn't do the job then try the same thing with initial-frame-alist instead (or in addition).
If you use Icicles then you can use command icicle-select-window to switch to windows by name, using completion.
icicle-select-window is an interactive compiled Lisp function in
Select window by its name.
With no prefix arg, candidate windows are those of the selected frame.
With a prefix arg:
What Org emits here is a printed representation of an otherwise opaque window object. While you can serialize a window to a string, you cannot go back from the string to the window. You can recognize such data types by their printed representation looking like #<...>, see https://www.gnu.org/software/emacs/manual/html_node/elisp/Printed-...
This is a snippet from @arne-babenhauserheide's site for making the frame urgent in X11, while it works it's not portable.
(defun my-frame-urgent-hint-set--for-x11 (frame arg &optional source)
"Set the x11-urgency hint for the frame to arg:
- If arg is nil, unset the urgency.
- If arg is any other value, set the urgency.
If you unset the urgency, ...
Are you sure that you don't have multiple frames in the same "tty window"? Does this doc help explain how to move among multiple frames when Emacs is in a text terminal?
On a text terminal, Emacs can display only one Emacs frame at a time.
However, you can still create multiple Emacs frames, and switch between
them. Switching frames on these ...