New to Arduino - asking about production path

Hello all,

I am new to Arduino.
I have designed a system for a customer based upon the Metro M4.

For the production version I want to design a custom PCB using the Atmel processor on the M4.
If I do this will I be able to easily use all the code I developed with the Arduino IDE?

I am worried about the bootloader, operating environment, etc.

Is this a seamless process?

Any input is appreciated!

Thanks,
Dante

Provided that you are experienced in PCB design for 120MHz and add all the required components, the software will run as expeced on a properly cloned hardware.

Is the firmware (OS, bootloader...) freely available or do you need a license for using it?