PATHINFO permalinks (starting with /index.php/) don't play well with custom tag/category prefixes.
example:
Permalinks:
/index.php/%postname%/
Category Prefix:
/topic
Tag Prefix:
/taxonomy
Issues:
- "You should update your .htaccess now." message is flashed, but nothing is provided to copy/paste
- Tag and Category URLs do not work.
- Even if you figure out what should be in .htaccess, paging for categories and tags wil be broken
All of the above happen because we now have a mix of PATHINFO and mod_rewrite permalinks. Permalink structure should be the authoritative PATHINFO/mod_rewrite decider. If /index.php/ is at the start of the permalink structure, it should also be automatically (and maybe silently) added to the front of the category/tag prefixes.
This is an issue for 2.2.1 as well (although obviously only for categories).
