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I have set up a theme that started off as a copy/paste of twenty-thirteen, because I'm familiar enough with that theme and would like to build from something I am familiar with.

That theme includes archive.php and category.php template files.

I have Permalinks set by postname.

In trying to fit an outside design to this theme, I have discovered that template that is in use when I select the categories tab (which should list out an archive or categories), the index.php file is the one in use.

Reading this article, both category.php and archive.php should take precedence. What am I doing wrong?

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Are you sure the webserver has access to those files? Permissions should be 644. –  Nabil Kadimi Aug 7 '13 at 23:48
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