Custom app in wordpress subfolder

Use .htaccess file on the same subfolder:

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /subdirectoryname/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /subdirectoryname/index.php [L]
</IfModule>

Thanks to:
https://wordpress.stackexchange.com/questions/20152/cannot-access-non-wordpress-subdirectories-as-wordpress-overrides-them-with-a-40