Best way to interop between the arduino and linux env of the Arduino Tre and Yùn

I'm working on a library for the Arduino TRE (and maybe YUN) and need to talk to a process running in the linux environment, i'm still not really sure of which way is the best to do communication between them, can i start a web server on the linux side and access that from the arduino code, or is using the serial port the best way?

(On a recent hack on the YUN i used the Console library to manipulate files in the linux file system and was able to send commands back and forth that way, but that feels like a very bad practice...)

Another related question, how would i distribute a library requiring binary code in the linux environment, i was thinking of letting the constructor check if the binaries are installed and if not install them, that doesn't seem that optimal since i need to keep the potential large binaries in the arduino code space :/

Any suggestions are welcome, i haven't really seen any libraries released like this yet.

http://forum.arduino.cc/index.php?topic=191820.msg1679588#msg1679588

Plan A: Disable the serial console from UART. 0.5Mb/s

http://forum.arduino.cc/index.php?topic=191820.msg1716261#msg1716261

Plan B: Force AR9331 to device mode from Host mode

http://forum.arduino.cc/index.php?topic=191820.msg1722207#msg1722207

Plan C: Wire one more PHY/Mac 100Mb/s

http://forum.arduino.cc/index.php?topic=191820.msg1722209#msg1722209

Plan D: I2C between CPU and MCU

http://forum.arduino.cc/index.php?topic=191820.msg1722210#msg1722210

Plan E: SPI between CPU and MCU

http://forum.arduino.cc/index.php?topic=280585.msg1977514#msg1977514

Plan F: Tre has 2 PRUs (The Programmable Real-time Units) which is far over powerer than Atmel ATmega32u4.lus it directly connnect with CPU BUs.