URL structure
The file structure of each content set directly impacts the URL path of each page. The directory structure you give docs-builder is the directory structure it produces.
Paths are relative to your docset.yml file, not the repository root. For example, if docset.yml is in ./docs/ and a page is at ./docs/a/b/c/my.md, its URL path is /a/b/c/my.
This is true for isolated builds (docs-builder serve) and codex environments. In assembler builds, the assembled site can change this path with path_prefix in navigation.yml.
Navigation order is set in docset.yml and toc.yml files, not by directory or file naming. See Navigation to learn more.