docs: centralize documentation under docs/

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)

.agents/skills/nix-config-desktop/SKILL.md

@@ -49,7 +49,7 @@ Store (needs the user to run `just niri`):
 - Noctalia per-host override: `home/hosts/linux/<dir>/noctalia.toml` (`host-<host>.toml`)
 - fcitx5 profile and addons: `home/linux/gui/base/fcitx5/`
 - vinput (voice input): `home/linux/gui/base/vinput/` (tag-pinned: the `fcitx5-vinput` row in
-  WORKAROUNDS.md §Pins)
+  docs/WORKAROUNDS.md §Pins)
 - Interface a net-speed widget reads: `home/hosts/linux/<dir>/noctalia.toml`
   (`[widget.net_rx]`/`[widget.net_tx]` `interface`)
 - `$HOME` state that must survive: `hosts/<dir>/preservation.nix` (tmpfs root; `12kingdoms-shoukei`

.agents/skills/nix-config-new-host/SKILL.md

@@ -38,9 +38,9 @@ in [hosts/README.md](../../../hosts/README.md).
   `outputs/x86_64-linux/src/k3s-test-1-worker-1.nix`
 
 A MicroVM guest is also registered in its VM host's `microvm.nix`; deploy it with the procedure in
-WA-026 of [WORKAROUNDS.md](../../../WORKAROUNDS.md), not `just microvm-deploy`. On a VM host with
-the `br0` bridge it also needs a `systemd.network.networks` unit that attaches the guest's tap to
-`br0`; the tap name comes from the guest IP (`192.168.5.116` to `vm116`). Some guest outputs also
+WA-026 of [WORKAROUNDS.md](../../../docs/WORKAROUNDS.md), not `just microvm-deploy`. On a VM host
+with the `br0` bridge it also needs a `systemd.network.networks` unit that attaches the guest's tap
+to `br0`; the tap name comes from the guest IP (`192.168.5.116` to `vm116`). Some guest outputs also
 expose a Colmena node for evaluation or other workflows; do not assume the physical-host deployment
 is done through Colmena.
 

.agents/skills/nix-config-update/SKILL.md

@@ -36,8 +36,8 @@ deploying the result to any host.
 - `just test` is green _before_ the update, so you have a baseline to compare against. It and every
   eval fetch the private `mysecrets` input over SSH; without that access they hang instead of
   failing.
-- Check [WORKAROUNDS.md](../../../WORKAROUNDS.md) for the inputs and recipes you are about to use;
-  an active row that names one of them replaces its command here.
+- Check [WORKAROUNDS.md](../../../docs/WORKAROUNDS.md) for the inputs and recipes you are about to
+  use; an active row that names one of them replaces its command here.
 - Enough disk for the new closures: `df -h /nix/store`. Broad nixpkgs bumps pull a lot.
 - Know what will move and choose the narrowest recipe that does the job.
 

.agents/skills/nixpkgs-patched/SKILL.md

@@ -3,7 +3,7 @@ name: nixpkgs-patched
 description:
   Use when temporarily carrying an unmerged nixpkgs pull request or commit in the personal
   ryan4yin/nixpkgs fork, updating the nixos-unstable-patched branch, or consuming that branch from
-  this nix-config flake, including a WORKAROUNDS.md row whose removal condition is carrying the
+  this nix-config flake, including a docs/WORKAROUNDS.md row whose removal condition is carrying the
   patch.
 ---