So I have just installed bedrock but when I go into Appearance > themes it is bringing up the themes from /web/app/wp/wp-content/themes rather than /web/app/themes
Sounds like a server config. What server technology are you using? You’d need write your virtual hosts (Apache) or server blocks (nginx) to serve the website from the path including .../web.
The one mu-plugin included with bedrock https://github.com/roots/bedrock/blob/master/web/app/mu-plugins/register-theme-directory.php registers the themes from the actual WP install for you. If you remove that file then those won’t show up. As long as you didn’t modify the application.php file at all to possibily mess with the changes it makes as far as your wp-content folder are concerned it sounds like possibly your theme style.css file may not be set up correctly to register that theme as a usable theme.
Actually isn’t it the opposite? If the autoloader doesn’t register app/themes/yourtheme then the mu-plugin looks in the default directory for themes?
So @nadge perhaps you just need to login to the Dashboard and set your custom theme as active? Pretty sure that most of the time when I set up a fresh install of Bedrock that 2015 is usually installed and active as the default theme.
It was just stupid issue not related to bedrock or my environment in the end. I was cloning bedrock from a private repo and the creator of the repo had gitignored the wp-config.php meaning that wordpress generated its own. After comparing the two repos i found the problem.
As it worked on the repo creators windows machine this was driving me crazy.