Is there going to be an update to the MySQL stack so that it can run 5.1 or is it safe to update the MySQL to 5.1 in this appliance? Any gotchas I need to look out for?
The next TKL release will be based on Ubuntu Lucid/10.04 which includes MySQL Server 5.1 in the repositories (see full package details here). I suggest that you hold out for now if you can, especially as TKLBAM will make migration a snap. There is no clear timeframe for release though (just as soon as they can) so if you urgently need 5.1 then you may need consider installing via an alternative method.
Off the top of my head, choices you have are (in the order I'd possibly consider them):
If you can't wait and wish to press ahead with one of these methods then I can probably give you a few more pointers.
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