Is it feasible?
Instead of browsing Apps, we browse .HEX files and each hex and a little description of which pins to use (what goes where) press a button and the program gets automatically downloaded and then uploaded (seamlessly) ...
is AVRDude standalone? (IE, copy the exe and nothing else) if so, avrdude could be used as a resource file ....
Good thought but...ONe thing here while you prototype and do etc testing stuff you change a lot and many times these lot of changes are like moving the pin from digi 4 to 5 now with hex files nothing could be changed at all!
There are sometimes that you can't just work with that pin ]
Bugger...
If pins were somehow able to by dynamically assigned somehow (I thought a script but you'd also have to upload it to the board with it)
shame....
Well you can add dip switches that are read when the processor boots up to select between a few fixed choices.
shame....
Keep on ..keep on.. BrainStorming, It takes an Idea and the will power to execute it to change lives upside down and effect positively in society.
I keep a doc handy always with me whereever I go wherein I write at the very same time the Idea which I get.
It's count is now 18, hell of a count to turn life upside down for Good 
HEX file store for homework.
This kinda exists already.
Google for "Arduino sketch". 
You do have to compile it yourself, but in return you can edit it to use any pin(s) you'd like!