Like why there is a resistor to the reset pin when the atmega support 5v and the VCC is 5V ?
Learn the basics of transistors and other discrete components first.arduino specifies source and sink current capabilities for outputs, to understand that properly you need to understand basic transistor operation first.
Do not waste time trying to understand arduino diagrams.
This is more of a electronic design question than a schematic reading question.
For me, they are terrible examples of schematics.
It is the common language we should all speak.