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I made a custom theme for my site which used the 2012 Q2A, and with a separate css and functions file.  Are these files going to be deleted if I upgrade to the latest theme?  What backups do I need to make, will things be incompatible, etc.  Also does spam still happen in the latest update.  I'm getting a lot of spam users.  Thanks.

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If your theme has a different name from any of the defaults (Classic, Candy, Snow, SnowFlat) then upgrading will not touch your theme. If you have modified one of those core themes then there are two options:

  1. Rename your theme to something else and re-select it in admin. You might also want to look at the theme you cloned in case there is anything new you want to add to your theme.
  2. Back up your theme, upgrade everything then reapply the changes you have made.

Regarding spam users, the new reCaptcha in 1.7 has stopped spam users on my site. So it's worked well for me.

molto grazie!