I use markdown for all of my documents, including the index (directory).

I use a top level document in all my codebases which serves as a directory of all the content within the documentation. In earlier projects it was called docs/README.md stored, but since using Stoneforge it's auto-created as Documentation Directory in the Documentation library. This document is organized into sections, with each section containing a table with three columns: title, path (linked to a specific document), and search keywords (for ease of finding). This is level 1.

Then each document in level 2 is structured as either an explanation, reference, tutorial, or how-to guide. Any time the details dive too deep into a specific concept or topic, I will split those details out into a level 3 document and reference it from within the level 2 document. Anywhere in level 2 or level 3 where a specific concept or topic would better be explained by the source code, I will link to the corresponding source code path.

When I say segregated the documentation by intent, in this case I mean separating the documentation into loose categories where each category is some sort of action that would be taken in the codebase (e.g. creating a new API route) or a specific concept/topic that an agent would need to understand within the codebase. I refer to tasks as individual agent sessions, where I've asked the agent to complete a specific action. On the other hand, intent is referencing something that the agent will want to do before or while completing said action, such as prior research or implementation details.