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What happens after a link is entered in the admin section and before a build is done? Is it the "add link" or the "build all" that places it in the database? I imagine the build only affects the category pages and the like.When you add a link from the admin section, it is placed directly into links.db. It will not go into url.db until the pages are rebuilt. So you can have more records in links.db then you have in url.db between builds.
The same is true when a user adds a record. The record goes into validate.db until you validate it, then it is moved to links.db but still will not appear in url.db until you rebuild the pages.
I hope this helps.