EPrints Ingredients
EPrints Ingredients were added in EPrints 3.4 as a means of providing complex functionality that was not suited to being provided by Bazaar plugins with their one-click install. This is because certain functionality (e.g. Coversheets) requires both EPrints and non-EPrints dependencies and complex configuration to be useful.
EPrints Zero includes the bazaar ingredient by default and it is enabled in the publication flavour's inc file. From EPrints 3.4.3, a jquery ingredient is included to package a known version of jQuery. This is not enabled in the publication flavour's inc file, as it only need be enabled if you intend to use jQuery within your repository for specific branding requirements.
From 3.4.4 a prototypejs ingredient is included, which is also enabled in the publication flavour's inc. This must be added to your repository's flavour's inc file if you are upgrading from an earlier version of EPrints 3.4, as it includes the Prototype and Scriptaculous JavaScript libraries underlying EPrints' JavaScript API. The reason for the moving to an ingredient is so that in future EPrints' JavaScript API needn't be tied to a specific JavaScript library and also to simplify copyright and licensing as these files are not subject to EPrints' copyright and license statements.