I too am facing the same issue. I'm using Firefox on a Windows 8 computer. I thought I had all the plugins necessary to upgrade. I did the online method that converted it to TW5. It just opened everything up and anything under the [[Tiddly Name]] format doesn't work as a link anymore. I wish I had a correction for you, but I'm stuck as well.
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Ah! I suggest making this more explicit. Since TW5 is now what one sees on tiddlywiki.com users of Classic will likely jump first to the upgrade instructions thinking they can upgrade classic tiddlywiki; despite the note on the HelloThere tiddler. I know I did. A note at the begining of the Upgrading tiddler that this applies to TW5 upgrades, a caution about thinking Classic TW can be upgraded, and perhaps a link to a a tiddler on what sorts of massaging existing Classic content will need (personally I use few plugins) would go a long way toward preventing disappointment.
Thanks for all the hard work; I've been a TiddlyWiki user since 2006 and look forward to the next 25 years.
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