This change definitely makes an online add-on manager more important, but for now everyone has the file "Server_EnableAllAddons.zip" in the screenshots directory as a temporary fix.
Add the following to the bottom of config/server/prefs/ADD_ON_LIST.cs to enable this enable all add-on:
$AddOn__Server_EnableAllAddons = 1;
Typing quit(); in the server's console will write out the entire list of installed add-ons to config/server/prefs/ADD_ON_LIST.cs. Useful for disabling certain add-ons.
Easier to move add-ons into another folder (like "Add-ons/disabled") to disable them.