just a little background for the (bi)curious

modutils-2.4.x provided a way for the user to customize 
things: /etc/modules.conf.  here users could control aliases and options and 
do all sort of neat tricks when loading/unloading modules.  the problem was 
that it didnt allow for packages to easily provide their own little snippets.  
should all those packages get folded into modules.conf ?  should you just 
grep/cat the file onto modules.conf ?  it's a nightmare.

so distros invented /etc/modules.d/.  now packages could manage their little 
pieces in this directory all by themselves.  the only problem was that 
modutils knew nothing of this.  it only knew modules.conf.  so distros had to 
write a little bit of glue where the conf file would be autogenerated by all 
the pieces in modules.d.  life, while better, is still kind of a pain.

when module-init-tools-2.6.x came out, peeps had learned from the past.  this 
means they changed two things: they included native support for a modprobe.d 
directory and they removed support for certain syntax deemed a pita.  this 
syntax change is why we have a new modprobe.d instead of just using the old 
modules.d.  however, the behavior is this: if /etc/modprobe.conf exists, use 
that, otherwise scan the modprobe.d directory.

now distros have yet another problem.  they've got packages that provide old 
snippets in /etc/modules.d/ and new snippets in /etc/modprobe.d/.  so in 
comes the lube again.  we automatically combine these directories and form an 
old-compatible modules.conf file and a new compatible modprobe.conf.  what 
would be ideal is for all of this lube to go away.  thus the latest 
update-modules script whines like a brat whenever a file is found 
in /etc/modules.d/.  by being proactive here and scuttling all the modules.d 
pieces, we will be left with only /etc/modprobe.d/.  that means no more 
annoying messages during boot "Updating modules.xxxx ..." which serves to 
slow things down.  on my amd64 system with very few files, that still takes 
~2 friggin seconds.

less stuff to do at boot => faster boot time => maintainers get a whiny notice
-mike