How are stems created?

[Phil Holmes]

I've been experimenting with alternative algorithms to create the flags used 
in mensural notation (see 
http://code.google.com/p/lilypond/issues/detail?id=3105), and part of the 
problem appears to be that the stems aren't attached symmetrically to the 
notehead.  I'm not sure whether this is deliberate or not, but I would like 
to look at it.  Could someone who understands this part of LilyPond explain 
how and where stems are added to noteheads (and, for completeness, flags are 
attached to stems)?

Thanks in advance.

An image of alternative flags, highlighted in red, is attached.

--
Phil Holmes

MenFlags.png
Description: PNG image