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

scripts/.tmp-index-coverage.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+"""Doctrine check: every dir has index.md; index links every sibling file/dir."""
+import re, sys
+from pathlib import Path
+kb = Path(sys.argv[1])
+issues = []
+dirs = sorted({p.parent for p in kb.rglob("*.md")})
+for d in dirs:
+    idx = d / "index.md"
+    if not idx.is_file() and d != kb:
+        issues.append(f"{d.relative_to(kb)}: no index.md")
+        continue
+    if not idx.is_file():
+        continue
+    text = idx.read_text(errors="replace")
+    linked = set()
+    for m in re.finditer(r"\]\((?!https?:|#)([^)#\s]+?)(?:#[^)]*)?\)", text):
+        t = m.group(1)
+        target = (d / t).resolve() if not t.startswith("/") else (kb / t.lstrip("/")).resolve()
+        linked.add(target)
+    # wikilinks too
+    wl_names = {m.group(1).strip().rsplit("/", 1)[-1] for m in re.finditer(r"\[\[([^\]|#]+)", text)}
+    for sib in sorted(d.iterdir()):
+        if sib.suffix != ".md" or sib.name == "index.md":
+            continue
+        if sib.resolve() not in linked and sib.stem not in wl_names:
+            issues.append(f"{d.relative_to(kb)}/index.md: does not link {sib.name}")
+    # subdirs of d linked as their index?
+    for sub in sorted(d.iterdir()):
+        if sub.is_dir() and (sub / "index.md").is_file():
+            subidx = (sub / "index.md").resolve()
+            dirref = sub.resolve()
+            if subidx not in linked and dirref not in linked:
+                # also accept link to sub/ or sub/index.md or wikilink to dir name
+                if not re.search(re.escape(sub.name) + r"[/)]", text):
+                    issues.append(f"{d.relative_to(kb)}/index.md: does not link subdir {sub.name}/")
+for i in issues:
+    print(i)
+print(f"index-coverage: {len(issues)} issue(s)")
+sys.exit(1 if issues else 0)

scripts/gen-keybinds.sh

@@ -27,6 +27,16 @@ KBD="${KBD:-$HOME/.config/niri/cfg/keybinds.kdl}"
 [ -f "$KBD" ] || { echo "error: no such file: $KBD" >&2; exit 1; }
 
 gen() {
+  echo "---"
+  echo "type: reference"
+  echo "title: Niri Keybindings"
+  echo "description: Live keybinding cheat sheet generated from $(basename "$KBD") — do not edit by hand."
+  echo "tags:"
+  echo "  - niri"
+  echo "  - keybindings"
+  echo "generated: { by: scripts/gen-keybinds.sh }"
+  echo "---"
+  echo
   echo "# Niri Keybindings"
   echo
   echo "> GENERATED by \`scripts/gen-keybinds.sh\` from \`$(basename "$KBD")\` — do not edit by hand."