I am curious as to which of the standard directories that software outside
my control uses. For instance, logs is used by the web server. I am
interested in cleaning up the directory structure a little for the novice
UNIX user. Plus, I would like to know in case the experienced UNIX user
asks.

Below is a list of the start files to make your reply easier. I know you
are busy so I don't mind really short answers. Mostly I need to know if the
directory is expected to exist and by what. If you have this documented
already, point the way.

.domains = e-mail

This is for mail delivery. If deleted, no mail will be delivered. Do
not delete.

.mreply.rc = e-mail

This is for autoresponders, maillists, listservers, and packet
(e-mail-ftp) MREPLY stuff. If not needed, feel free to delete.

archive/ = ???

Used with MREPLY. Delete if not needed.

cgibin/ = ???

Can be used for cgi programs but doesen't have to be. Delete at will.

configuration/ = ???

Delete if not needed.

docs/ = harmless

Delete if not needed.

index.htm = starting web page

Replace with your own.

link/ = harmless

Not sure. Delete at will.

lists/ = ???

Used with MREPLY. Delete if not needed.

logs/ = web server

Web server logging. Do not delete

majordomo.cf = majordomo

Outdated. Delete.

random/ = looks harmless

Not sure. Delete at will.

readme.mreply = mreply (harmless)

Self explanatory.

sample2.mreply.rc = mreply (harmless)

If you are going to use MREPLY, use this instead of the .mreply.rc that
we give you. This one works better. Delete if not using MREPLY.

setup = harmless

Limited info regarding the setup of the account. Delete if desired.