You should never directly modify the source XML files that are installed by applications in the <MIME>/packages directory. Instead, modify the Overrides.xml file. This file has precedence over all other source XML files installed into the same packages directory. If you are an application author, then this rule does not apply. Application authors should create a new source XML file and place the file in the <MIME>/packages directory.
You can modify the MIME database for all users on the system or for a particular user depending on the location of the file you change. To modify the database for all users, make changes to the file Overrides.xml in the $XDG_DATA_DIRS/mime/packages directory. To modify the database for a single user, make changes to the Overrides.xml file in the $XDG_DATA_HOME/mime/packages directory.
After changes are made, you must always run the update-mime-database application with the directory location of the MIME database as the first parameter.