Permalinks are wrong when using the plain permalink structure

[keesiemeijer]

Permalinks for taxonomy archives and method post type posts are going to 404 pages because they use pretty permalinks even when the plain structure is set.

for example the link to the source file taxonomy page for /wp-includes/query.php should be /?wp-parser-source-file=wp-includes_query-php (if the plain structure is set). Instead it goes to /reference/files/wp-includes/query.php/

The same happens with method post permalinks. The method_permalink and taxonomy_permalink filter callbacks that change the permalinks do not use a check to see if pretty permalinks are used.

[keesiemeijer]

Add check for pretty permalinks

[coffee2code]

In 2965:

developer.wordpress.org: Check if pretty permalinks are in use before attempting to modify permalink structure.

Props keesiemeijer.
Fixes #1648.