The first Arduino was serial, and over the decade and a half, this has been the default way to upload code to an Arduino board. In 2008, support for in-circuit programmers was added, and later port detection was added. The latest version of the Arduino IDE adds something new: pluggable discovery. Now any protocol is supported by the Arduino IDE.
This feature is the brainchild of [Paul Stoffregen], creator of the Teensy. If you’ve ever used a Teensy, you’ll remember the Teensyduino application used to upload code to the board. The Teensy uses HID protocol instead of serial for uploading. After working to improve the integration between the Teensy and Arduino IDE, [Paul] stated extending the DiscoveryManager. After some discussion with the Arduino developers, this feature was then added to Arduino 1.8.9, released a month or so ago.
There are some issues with Pluggable Discovery, most importantly that it doesn’t yet exist in the Arduino Command Line Interface (yeah, that exists too). If you’re looking to contribute to Open Source, that would be a nice project to pick up.
With the right JSON, and configuration, it is now theoretically possible to extend the Arduino IDE to any sort of protocol. This means (again, theoretically), it’s possible to update the firmware in your DIY MIDI synth over SysEx message, or a parallel port, maybe. Someone is going to upload to an Arduino board over PCIe, eventually.