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.