I ran the patch for upgrading an OJS instance from 2.3.8 to 2.4.2, using the actual patch command and not the php tools/upgrade.php patch command. Then I ran the database upgrade using php tools/upgrade.php upgrade. The patch indicated there were some rejected files, whereas the database finished without any errors.
However, there are a few issues with the site now:
1. The "User Home" link in the main menu now goes to /index.php/index/user instead of /index.php/journalname/user. This means that the user is now shown the default template instead of the template that the journal editors have customized.
2. "Step 3" in the Journal Management -> Setup process returns a blank page (i.e. /index.php/journalname/manager/setup/3). Steps 1, 2, 4, and 5 work as expected -- it is only Step 3 that is not working.
FYI, the list of .rej files are as follows, in case it is related to the issues described:
Any pointers in the right direction are greatly appreciated.