The Codex is a structured reference for the world of a book: characters, places, invented terms and the relationships between them, stored in the project and linked to the prose rather than maintained in a separate document.
The fourteen categories
Characters, Locations, Factions, Magic Systems, Lore, Cultures, Languages, Timeline, Glossary, Lineages, Regions, Maps, Storylines and Items. Each category has its own fields, so a character entry and a location entry store different information rather than sharing one generic note format.
Tagging from the manuscript
Select a name in the prose and link it to its Codex entry. The link is stored against the text, so the entry lists the scenes in which it appears and the scene lists the entries it references. Neither list is maintained by hand.
The relationship map
Entries may be linked to one another, and those links are displayed as a map. It records the connections themselves rather than a description of them, so a change made to one entry is reflected wherever that entry is referenced.
Timeline, distinct from scene order
The Codex Timeline records the chronology of the world: a war, a founding, a disappearance. It is stored separately from the order in which scenes are told, so a non-linear narrative does not require a non-linear record of events.
Scope across a series
One Codex serves every book in a series. A detail established in the first book is available in the fourth without being re-entered, which is what keeps a long-running world internally consistent.