My interpretation of the problem is that the call to sit_for in 
    read_char is allowing the idle timers to run.These idle timers 
    (semantic-idle-core-handler) are doing a lot of work, and using 
    input-pending-p to allow user input to interrupt them.

Why is that a problem?

     The problem seems 
    to be that process-output and clipboard requests are not being handled 
    while Emacs is inside that sit_for,

Do you know that, or is that a guess?

If that is true, it is a bug already.  Process output should be
handled inside the sit-for; clipboard requests should either be
handled inside the sit-for, or cause it to wake up so they can be
handled.

However, I can see how process output would not be handled during that
timer function.  And if it only tests input-pending-p, it won't notice
that process output is waiting.  So maybe that is a bug.

Maybe the timer function needs to call accept-process-output.

Is that function in the Emacs distribution?  What package?


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