Review the output of the upgrade task carefully.
Many of the messages will identify obsolete files that can be deleted. Those don't need to be handled immediately, but should be noted for deletion towards the end of the upgrade process.
In some cases, the messages will say
>> config If you made some customization in this file, >> config please migrate the content to the configuration classes.
Most commonly, these will be config.php files. You should review each of these files, and if necessary, migrate the changes to either the ProjectConfiguration? class or ApplicationConfiguration? classes.
In other cases, the upgrade task will have determined that you have modified a file, and issue a slightly different message, such as
>> config You made some customization in the following file: ..../web/backend.php >> config Please, upgrade manually (new code appended as a comment)
In this case, the upgrade task has added the new code, facilitating the job of merging your code with the new versions.