If you are using Links SQL v.1.X, then all you have to do is the following:

1) Edit all the links in the header.txt file and other template files in the admin/templates folder.

2) Edit the Links.pm file. Put in the new folders/directories where your pages should be built.

3) Re-build your directory via ADMIN.GGI.

4) Delete all your old directories and files,

About the password required for the newsletter/subscribers, you'd have to edit the subscribe.cgi script and your EMAIL template files in the admin/templates folder.

Hope this helps.
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Buh Bye!

Cheers,
Me