Microcontroller (AVR) programming from smartphone

Hi Friends!
Briefly: considering ways of uploading code to microcontroller (particularly some Atmel's AtMega - same as used for Arduino) from the smartphone.
In details:
Programming MCUs (e.g. uploading firmware into their ROM) usually happens via
some proprietary interface (using SPI in case of AVR), or UART, or JTAG. This generally involves dedicated software on the side of computer and some hardware (USB to UART or dedicated "serial programmer").
Suppose we want to be able to write simple code using mobile phone - situation I met with my class of 15+ students with no dedicated lab having 15+ computers.
I tried creating a small system containing two parts: First - html web-page with a textarea to write assembly code, built-in AVRA assembly compiler (just compiled to javascript) - and some JS code which can "beep" the bits of the hex-file containing firmware (via audio). Second - bootloader for target MCU which uses ADC pin to "listen" to those beeps via direct wire connected to 3.5 mm audio jack plugged into smartphone - and "burn" incoming data into flash memory.
This works (if you are curious to try, it could be found in my github page by same username) - however there is a sudden issue: almost half of students use mobile phones without 3.5mm jack - as nowadays it is the era of wireless headphones already, I missed the fact!
So now I'm looking for further, alternative approaches. For example:
- attaching microphone to ADC pin instead of wired connector; code should be beeped out via built-in speaker of the smartphone (it would be a bit noisy class, of course) - I actually tried, but was not yet able to come up with signal recognition algorithm of good enough quality.
- blinking data with display and catching it with photo-transistor attached to ADC or digital pin, haven't tried for it seems like bitrate would be very low (even though we generally need to upload firmware of few dozens bytes).
Thus I'm open to any ideas / hints / articles on improving either of these two approaches - or perhaps something completely different which I may have missed.