The extensions are located in www/ext. The extension manager can be opened in SeedDMS in the admin are.
The pdf viewer has been moved into an extension which is shipped with 6.0.38. Did you activate it in the extension manager?
I guess SeedDMS is trying to create a preview of that large image and fails. Unfortunately, this prevents the listing of the folder where that document is located. There is currently no quick fix, but turning the creation of preview images off by taking out the line which adds the conversion service in inc/inc.ConversionInit.php. Are you familiar with PHP? How large is that picture?
E-mail notification broken
Well be fixed in 6.0.39
Can you check the error log of apache or php-fpm? Is there any issue reported on the page out/out.Info.php ?
There is no 'pear' in inc.Settings.php. Check out https://codeberg.org/SeedDMS/seeddms/src/tag/6.0.38/inc/inc.Settings.php
Your include has a space between /home/www-data/seeddms60x/www/ and ... Could that be the reason? I also wonder why /home/www-data/seeddms60x/www/pear is still in your include path.