I thank you for taking such effort to present this tutorial++. But I must I admit that I only skimmed over the code listings so I can't comment on the logic or syntax. This is not a code snippet which I can just simply get it and run it. Since this is a complete application, I'd like to rather see the actual application online to see how it works. So we know what to expect before trying. Especially you claim that:

it does work

I don't think using a large number of modules would be a problem because tutorials has levels of audience. We can say that this tutorial is aimed for intermediate users, not merely beginners.

I'd like also to point about the documentation you refer to. It's nice to tell that those docs are also available locally, because one isn't always connected to the Internet. I guess many intermediate users already know about this, but I'd considered it value added if you mention that users can access Apache docs via http://localhost/manual and MySQL docs, provided that it's installed properly by whatever Linux distro users use or installed manually, via¹:

$ info mysql
$ pinfo mysql
[download]

And about the line numbers.... You should know that codes in PerlMonks are meant for downloading so it can be run right away without any modification (additional step, even if you provide a nice snippet to remove them) on the text unrelated to the code logic or internal data. But, I also support the usage of line numbers in the tutorial code as guidance or reference of the explanation. In this case, it's good to provide other means to obtain the actual codes.

Each listing should start with their own number 1. And it's better for me as audience to see the explanations separated for each listing. So when you say, for example, "Simple.pm:10-15" as suggeted by eric256, I know for sure what's the context that particular saying in. In this case of this clear separation of the explanations, it's useful to make cross references by explicitly mentioning the listing name, or merely the listing number. Putting backlinks would also improve user experience so we can go back and forth between the listing and the text. For example:

Some text that refers to listing. The explanation contniues....

later in the listing....
Listing1: foo.pl - Back to text

 1: #!/usr/bin/perl
 2: use strict;
 3: use warnings;
 ...
[download]

The only benefit I can see by using continuation number is that I know right way that it takes around 270 LOCs to build such application in Perl (but the number is not such a big deal).

Hope you can find this useful. Once again, great effort!

Update
1: info and pinfo are pretty standard in Linux box. I don't know the equivalent tools for another OSes

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