the_permalink() broken when wp home and site home not the same

I have a site with wordpress installed in a subfolder. If I go with the default settings where both the entries in the WordPress Address and Site Address fields of the General Settings are the same, like https://localhost/mysite/wordpress, everything is fine. However, if I change Site Address to the site root (https://localhost/mysite), every link within WP that uses the_permalink() function fails and I get links like https://localhost/mysite/?p=18 instead of something that works like https://localhost/mysite/wordpress/?p=18.

How can I fix this?

Thanks – Joe