Yes, I do fully agree with your post. Foremost I would like to be able to use the mathematical functions. Second on my list would be a good import possibility, packaging would even be better.
If import of packaging doesn't come, then please a decent cutting and pasting mechanism in the Foldit editor.
This would be the easiest way to open up FoldIt to the masses.
PHP and Java in foldit?? For what reason?
All "external" things we need is few standard libraries and plain text files access.
Internals are well listed by Tlaloc (cant wait for bands over 20…).
Being able to use external scripting languages could allow you to a lot off things. Least of which would be abilities to create interface tweaks. Imagine a choice of Recipe managers or being able to have a choice of editors to create recipes instead of the native kludge editor. With php and javascript (not Java, close but sorta different) you would have file system access to create recipes that save settings and data betweeen instances.
Best of all you could real AI programs like GAs and Neural Nets that could apply from puzzle to puzzle.
The game becomes a whole different entity that way. It changes from a project on how people use foldit to how foldit itself evolves.