Nothing very hard to say about this upgrade but the guide found at this address is something incomplete.
I used the “standard install package” section but when it comes to copying configuration, modules and plugin from the old install directory the guide don’t mention all the paths needed to be copied.
What is suggested
cp moodle.backup/config.php moodle cp -pr moodle.backup/theme/mytheme moodle/theme/mytheme cp -pr moodle.backup/mod/mymod moodle/mod/mymod
Basically there are some other paths to search for missing code, plugin and modules to mantain in the migration.
You also have to search other directories to transfer in the following path.
moodle.backup/local moodle.backup/blocks moodle.backup/filter
Luckily enough the web updater warns you if something is missing and makes you aware of the path.