Is your WordPress .htaccess file causing problems with other files?

That’s the issue I ran into. I was building a WordPress site, and put a billing/invoicing app in a subdirectory of the site.

Well, the default rewrite lines (that WordPress added to the site’s htaccess file) were causing major issues for the billing script (AWBS). It was also causing problems with Apache password protecting of a directory. The WordPress rewrite would take over before Apache would invoke the username/password entry box.

It was a big mess. I spent a long time pulling my hair out over the situation.
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