docs: close OKF conformance gaps found by night audit

- references/okf-spec.md: replace v0.2 note with the deltas verified
  against upstream SPEC.md 2026-10-19 (timestamp->generated.at and
  # Citations->sources are the two breaking changes; trust fields and
  root-index okf_version are additive; bundle stays v0.1).
- index.md: restore the agentic-web-research section lost in the
  2026-08-28 rebuild and link log.md (index-coverage doctrine).
- gen-keybinds.sh emits OKF frontmatter so its generated artifact
  (tools/niri/keybindings.md, regenerated, 120 bindings) passes kb-lint;
  test added red->green.
- fix the two broken [[niri]] wikilinks (handy, noctalia-shell).

Refs #29

omp-docs/tools/noctalia-shell.md

@@ -429,7 +429,7 @@ noctalia msg templates-apply
 
 ## See Also
 
-- [[niri|niri/index.md]] — Compositor configuration
+- [niri](niri/index.md) — Compositor configuration
 - [[displays|displays]] — Display layout
 - [[cachyos|cachyos]] — Operating system documentation
 - [`noctalia msg --help`](https://github.com/Noctalia/noctalia) — Full command reference