An alternative to PR #515 ... #521
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Comment out forgotten debug messages.
In avr_ioport.c, AVR_IOPORT_OUTPUT could be misinterpreted as data, causing the USI test to fail. In avr_flash.c, do not drop IOCTLs for later handlers, that broke atmega88_example. In Makefile, restore the hex file needed by atmega88_hex. Also add test_atmega644p_signature_read.c so that the new firmware file is run by "make run_tests".
PWM output from timer was not modifying the PIN register.
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... that seems to fix the problem and preserves the benefits of the original change.
Merging this will also merge PR #520 as they both change the same code and there seems no way for them to be separate without creating a merge conflict on the second one.