This isn't a simple problem, but one suggestion about a
factor that you seem to be ignoring.
What are you using for version control? There are many
kinds of problems you need to deal with, and security is
only one of them.
Personally I would suggest having the data and some local
configuration nowhere near your cgi-bin for the simple
reason that it is nice to have your cgi-bin under the
control of CVS, and you don't want to check all of your
data files into CVS! Likewise it is good to have the
possibility of per user configuration information safely
out of CVS.
A lot of schemes are possible, but the simple step of using
some versioning scheme on important files saves many
headaches, makes it much easier for developers to work in
close cooperation. Just remember to commit and update early
and often...
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