Move standalone repository docs from the root into docs/ and add a documentation index that links the moved docs and the code-local runbooks.
Update Markdown links, source comments, and the root entry points to the new locations. Keep README.md and AGENTS.md at the root as required entry points.
Assisted-by: DeepSeek Harness (deepseek-flash)
* docs(skills): point nix-config-secrets at the private repo under ~/codes
Record where the private nix-secrets checkout lives and that agents should
do the mechanical secret work themselves, handing back only the
interactive/sudo agenix operations and pushes.
* docs(agents): add related repositories to nix-config
* chore(agents): adopt ~/src for source checkouts
Move third-party/source checkouts from ~/codes/src to ~/src so the home
layout reads as three siblings: ~/codes (personal), ~/work (work),
~/src (checkouts). Preserve and back up the new path, and update the
global rule and the two nixpkgs skill references.
* docs(agents): tighten the code layout rule
* docs(agents): fold the work-confidentiality note into the layout line
* docs(agents): base the confidentiality rule on repo visibility
* docs(agents): drop the stale KubeVirt mention