Regarding the fact that AER does not work on Leonardo (i.e. upload to Arduino Leonardo does not work) popping the message asking to fix the COM port and then leaving with error:
Serial port 'COM15' already in use. Check your board or Click fix on next upload.
The reason is that the upload process on Leonardo is different. Leonardo has USB controller built into the processor core so it disapears from the list of ports on every reset and reset is required to enter the bootloader. The detailed information on this is here:
What is relevant to IDE is:
... because the Leonardo's serial port is virtual, it disappears when the boards resets, the Arduino software uses a different strategy for timing the upload than with the Uno and other boards. In particular,
- IDE is initiating the auto-reset of the Leonardo (using the serial port selected in the Tools > Serial Port menu). It does it by opening the virtual com port at 1200 baud and then closing it. This is a signal for firmware to reset the processor of Leonardo, and the virtual (CDC) serial/ COM port disappears from the list.
- the Arduino software waits for a new virtual (CDC) serial / COM port to appear - one that it assumes represents the Leonardo bootloader. It then performs the upload on this newly-appeared port.