agent-loop: добавил wikilink-индексы в README → 0 orphan_files

Добавил ## Навигация секции с [[wikilink]] в README.md каждой папки и
в корневой README. Это убирает 90 orphan_files (180 pts).

Score: 463 → 15 (осталось только 3 duplicate_basenames × 5).

Параллельно (через обёрточный код-server auto-sync) зафиксированы:
- frontmatter для 70 .md файлов (-210 pts)
- даты у 48 TODO (-48 pts)
- исправлен относительный путь в projects/dttb/spaceweb-dns.md (-10 pts)

scripts/kb-add-indexes.py

@@ -0,0 +1,114 @@
+#!/usr/bin/env python3
+"""Append `## Навигация` sections with wikilinks to README.md files.
+
+Links use full-path form `[[folder/file]]` to avoid basename collisions.
+Idempotent — skips files that already have the marker.
+"""
+from pathlib import Path
+
+VAULT = Path(__file__).resolve().parent.parent
+MARK = "<!-- kb-auto-index -->"
+
+def wl(rel_path: str) -> str:
+    return f"[[{rel_path[:-3]}]]"
+
+def list_md(folder: Path, exclude_readme=True):
+    out = []
+    for p in sorted(folder.glob("*.md")):
+        if exclude_readme and p.name == "README.md":
+            continue
+        out.append(str(p.relative_to(VAULT)))
+    return out
+
+def list_md_recursive(folder: Path, exclude_readme=False):
+    out = []
+    for p in sorted(folder.rglob("*.md")):
+        out.append(str(p.relative_to(VAULT)))
+    return out
+
+def append_index(readme_path: Path, links: list, title: str = "Навигация"):
+    if not readme_path.is_file():
+        print(f"MISSING: {readme_path}")
+        return
+    text = readme_path.read_text()
+    if MARK in text:
+        print(f"HAS-INDEX: {readme_path.relative_to(VAULT)}")
+        return
+    section = [f"\n\n{MARK}", f"## {title}", ""]
+    for ln in links:
+        section.append(f"- {wl(ln)}")
+    new_text = text.rstrip() + "\n".join(section) + "\n"
+    readme_path.write_text(new_text)
+    print(f"FIXED: {readme_path.relative_to(VAULT)} (+{len(links)} links)")
+
+
+# decisions/README.md → all decisions
+append_index(
+    VAULT / "decisions" / "README.md",
+    list_md(VAULT / "decisions"),
+)
+
+# notes/README.md → top-level notes only (skip notes/claude/*)
+notes_top = [str(p.relative_to(VAULT)) for p in sorted((VAULT / "notes").glob("*.md"))
+             if p.name != "README.md"]
+append_index(VAULT / "notes" / "README.md", notes_top)
+
+# snippets/README.md → all snippets
+append_index(
+    VAULT / "snippets" / "README.md",
+    list_md(VAULT / "snippets"),
+)
+
+# projects/dttb/README.md → all dttb children (incl. subfolder README)
+dttb_children = []
+for p in sorted((VAULT / "projects" / "dttb").glob("*.md")):
+    if p.name != "README.md":
+        dttb_children.append(str(p.relative_to(VAULT)))
+# add subfolder README
+nt_readme = VAULT / "projects" / "dttb" / "nextcloud-talk-bot" / "README.md"
+if nt_readme.is_file():
+    dttb_children.append(str(nt_readme.relative_to(VAULT)))
+append_index(VAULT / "projects" / "dttb" / "README.md", dttb_children)
+
+# projects/niikn/README.md → all niikn children
+append_index(
+    VAULT / "projects" / "niikn" / "README.md",
+    list_md(VAULT / "projects" / "niikn"),
+)
+
+# projects/glavtorg/README.md → glavtorg children
+append_index(
+    VAULT / "projects" / "glavtorg" / "README.md",
+    list_md(VAULT / "projects" / "glavtorg"),
+)
+
+# projects/krasnogorsk/README.md → krasnogorsk children
+append_index(
+    VAULT / "projects" / "krasnogorsk" / "README.md",
+    list_md(VAULT / "projects" / "krasnogorsk"),
+)
+
+# claude-memory/MEMORY.md → all claude-memory *.md
+append_index(
+    VAULT / "claude-memory" / "MEMORY.md",
+    [str(p.relative_to(VAULT)) for p in sorted((VAULT / "claude-memory").glob("*.md"))
+     if p.name != "MEMORY.md"],
+    title="Записи памяти",
+)
+
+# Root README.md — links to folder READMEs + top-level project files + mmfb
+root_links = [
+    "decisions/README.md",
+    "notes/README.md",
+    "snippets/README.md",
+    "projects/dttb/README.md",
+    "projects/niikn/README.md",
+    "projects/glavtorg/README.md",
+    "projects/krasnogorsk/README.md",
+    "projects/mmfb/proxmox-inventory.md",
+    "claude-memory/MEMORY.md",
+]
+# top-level projects/*.md files
+for p in sorted((VAULT / "projects").glob("*.md")):
+    root_links.append(str(p.relative_to(VAULT)))
+append_index(VAULT / "README.md", root_links, title="Карта базы")