arduino_uno_r3_from_scratch
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RESET circuit is wrong
The RESET circuit on your schematic is wrong when compared to the Atmel AppNote AVR042. In normal operation, you have 5V - 0.7V = 4.3V at the RESET pin, but it doesn't provide any over-voltage protection. And when pushing the reset switch, you will have a short circuit to ground from 5V_LDO through D7 and the switch, without any resistance.
This picture below is copied directly from the AppNote AVR042 - AVR Hardware Design Considerations