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)
microvm.nix's sshSwitch step runs nix-store --load-db against the guest's
read-only virtiofs /nix/store and dies there, so the recipe installs the
runner on the physical host and restarts microvm@<guest> instead.
`just test` has enforced the suite result since #350: the recipe raises unless
`evalTests` is `true`, so a zero exit already means pass. Update the places that
still described the old raw-`nix eval` behaviour: AGENTS.md, README.md,
SECURITY.md, outputs/README.md, and the nix-config-debug / nix-config-new-host /
nix-config-update skills.
The exit-0 caveat is kept only where the raw `nix eval .#evalTests` command is
documented, because that command genuinely exits 0 even on `false`.