Whether you compile manually with a Makefile (or Arduino-Builder) or in the IDE, the end result is a HEX file. This is a text file describing the data to load into the flash memory.

You then use avrdude to install it into the Arduino - either from the IDE or by running it manually (or specifying it in your Makefile, etc).

A Makefile doesn't produce an executable. A Makefile is merely a recipe - a set of instructions - telling the make program which programs to run (gcc, avr-ggc, etc) and in what order (and with what flags) to compile your code.

There are many Arduino Makefile projects out there that do it all for you.

Whether you compile manually with a Makefile (or Arduino-Builder) or in the IDE, the end result is a HEX file. This is a text file describing the data to load into the flash memory.

You then use avrdude to install it into the Arduino - either from the IDE or by running it manually (or specifying it in your Makefile, etc).

A Makefile doesn't produce an executable. A Makefile is merely a recipe - a set of instructions - telling the make program which programs to run (gcc, avr-gcc, etc) and in what order (and with what flags) to compile your code.

There are many Arduino Makefile projects out there that do it all for you.