the best and also most annoying method right now is online authentication check against a live database somewhere on your server, so every time register, it check against the server if the code has been previously active or not. and the software required active connection to your server to...
301 redirects from old pages to new pages if URL structure is different.
some of the wordpress theme has built in rich snippets for google, has your codeigniter implements those? sitemap, RSS feed, social media meta tags, H tags semantic order, GEO meta tag, cache, gzip, expired headers...
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