Christiaan:

> I could implement that using a hidden preference. I am really
> hesitant to have this by default.

As long as there is a simple and fast way to set it that would be ok. 
For example, if I could call a script that set things or unset them
later from the command line it would work.

I have become allergic to hidden controls.  Magical controls that
require one to mouse over special places on a display can be
impossible to discover or remember.  Instead how about having a
section 'Advanced controls' and making everything directly visible? 
Then people won't be wondering.  (There are some controls for setting
Skim to display a certain way - I can't even say what they are since
they are invisible - but having them explicit would save me a lot of
puzzlement.)

> How large should that dot be? About the size of the close button
> (which you get when you move the mouse to the bottom)? Or half that?

I looked at the mouse presentation with skim.  On text it is an I beam
or a pointer hand.  On the bottom it becomes an open hand.  So I don't
know what you are seeing or how to reproduce it.  How about making it
controllable?  The normal mouse pointer has size controls.

From Finder Help for 'pointer':

---
Magnify the mouse pointer on Mac

If you have difficulty seeing or following the mouse pointer when it moves—or 
it changes to an insertion point, crosshair, or other shape—you can increase 
its size.

On your Mac, choose Apple menu  > System Preferences, then click Accessibility.

Open Accessibility preferences for me

Click Display, then drag the Cursor Size slider to the right to make it larger.
---

Thanks for your work on this fabulous program!!

Tom

  Thomas D. Schneider, Ph.D.
  Senior Investigator
  National Institutes of Health
  National Cancer Institute
  Center for Cancer Research
  RNA Biology Laboratory
  Biological Information Theory Group
  Frederick, Maryland  21702-1201
  [email protected]
  https://alum.mit.edu/www/toms


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