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I just updated to 3.7.13 using the manual method,
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Notice I state as of 3.7.12 I recommend using the automatic method…(as long as you store you images outside the theme folder.
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Letter J says "verify URL Names in the options". Which options are you referring to?
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any option where you were using it.
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I noticed that on my dashboard it no longer tells me what version I am using
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this is a'feature' of WordPress, not theme related - you have to go into details (I don't like it eithor)
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in Manage Themes, can I get rid of the old version, once I'm sure all is well?
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Yes
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How does the new atahualpa version know what my settings for the old one were
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the atahualpa settings are stored in the database so they survive updates./