An Arduino timer question

I have been delving (groping blindfold, more accurately) into the Arduino compiler adaptation code to try to determine how it handles the switch-over between its pwm activities, its set-I/O-to-output activities, its set-output-high (or low) activities, and any user pwm or I/O activities. For example, when manually setting a port pin to pwm, what information does ...

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from Electronics Weekly https://www.electronicsweekly.com/blogs/engineer-in-wonderland/arduino-timer-question-2018-02/