bug#54371: 29.0.50; read-char does not reset idle timer in some cases

[Ignacio Casso]

Hello,

If I evaluate the following snippet, after 3 seconds Emacs prompts me
for a character and prints nil.

  (defun my-test ()
    (read-char "> " nil nil)
    (message "%s" (current-idle-time)))

  (run-with-timer 3 nil 'my-test)

However, if I evaluate the following snippet instead, where the last
argument of read-char is changed to the number of seconds the prompt
should wait at most for user input, it prints (0 K _ _), where K is 3
seconds plus whatever time in seconds you took to answer the
prompt. This means that right after reading a character from user input
Emacs still thinks it has been idle for a while.

  (defun my-test ()
    (read-char "> " nil 10)
    (message "%s" (current-idle-time)))

  (run-with-timer 3 nil 'my-test)

This is the reason behind a bug that occurs when resolving the running
org clock after some idle time, for which I have seen reports more than
10 years old but not as much discussion as I would expect. This makes me
think that Emacs does not behave like this for most systems and the
problem is particular to my setup. My setup should not be particular in
any sense however, just an Ubuntu 20.04 with default and standard
packages. Emacs' is the only configuration I have ever tweaked in my
machine, and this happens also with "emacs -Q", so it's not that.

Can you please evaluate the second snippet to try to reproduce this in
your machine? If you can't, I will be happy to provide any other
information of my machine that you think may be needed to reproduce
this, or to follow whichever steps you suggest to try to debug this
myself (I would have tried already but all functions involved are
written in C or too low-level).

Regards,

--Ignacio