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Under /sites/all/themes there are two folders called atlas and atlas.backup. Drupal 7 is pointing to atlas.backup and I don't understand how Drupal knows which theme folder to use.

I want Drupal to use the atlas folder, rather than the atlas.backup one.

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    I strongly recommend using version control (e.g., git) for backup rather than duplicating files. Oct 11 at 6:27
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You should never, ever keep a duplicate/backup copy of any theme or module anywhere under /sites/all. You can't control which copy Drupal will find first, and you may actually be using parts of both.

You must move the backup copy outside of Drupal root. You will need to clear your caches and perhaps rebuild your registry after you do that.

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