Attached is the example above arranged in LilyPond (without the feature "neumes close together"); as the forum doesn't allow me to post .ly files, please check the template out here: https://gist.github.com/3657434
LilyPond (.ly) files, just like TeX (.tex), LaTeX (.ltx), GABC (.gabc), and several other kinds of files are nothing more than text files. So, before uploading, just rename the .ly file with a .txt extension ... or make the extension .ly.txt (so downloaders know it is secretly a LilyPond file). Once downloaded, the extension can be changed back to .ly.
Agree that the third feature is difficult, because as far as I know it can't be automated. You would have to manipulate each note's horizontal position manually. It's pretty annoying.
Here is an alleluia I put together last year. The finished product looked like this.
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