Add librarian Stage 1 citation checker with ignore list

scripts/librarian_check_citations.py extracts file:line references from
inline-code spans across docs/**/*.md and verifies each path exists
(and, if cited with a line number, is within range). Skips
docs/archive/ and docs/plans/archive/ which are read-only by policy.

Caught one real drift in docs/research/optimization_sequencing.md: the
note pointed at docs/plans/amp_trainer.md, which had moved into
docs/plans/archive/.

scripts/librarian-ignore.txt holds fnmatch globs for citations that are
intentionally future-tense (planned files described in the plan docs
themselves). Used sparingly so the checker stays useful as a drift
signal.

Updates docs/plans/librarian.md Progress + Next Step. Next concrete
step is a thin scripts/librarian.sh orchestrator over both checkers.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

docs/plans/librarian.md

@@ -121,12 +121,30 @@ operator applies the patch.
 - ✅ Prompt moved: `.claude/agents/librarian.md` →
   `scripts/librarian-prompt.md`. Claude-specific subagent registration
   removed.
+- ✅ Stage 1, piece 1: `scripts/librarian_check_links.py` (lychee
+  wrapper). Caught one stale README link on first run (commit
+  `b9bbb4f`).
+- ✅ Stage 1, piece 2: `scripts/librarian_check_citations.py` (custom
+  `file:line` citation checker over inline-code spans). Skips
+  `docs/archive/` and `docs/plans/archive/`. Ignore list at
+  `scripts/librarian-ignore.txt` for intentional future-tense
+  references. Caught one real drift in
+  `docs/research/optimization_sequencing.md` (path moved into
+  `docs/plans/archive/`).
+
+## Stage 1 Remaining Checks
+
+- Stale plans (mtime + git-log staleness heuristic).
+- Promotable archive entries (deferred to Stage 2 — heuristic vs LLM
+  judgment is the open question).
+- MEMORY.md drift (index lines vs target file `description:` frontmatter).
+- Duplicate prose (high-overlap pairs across archive vs research).
+- Oversize files (>500-line soft cap from AGENTS.md).
 
 ## Next Concrete Step
 
-Build a minimum viable Stage 1: port coolrl's `check_doc_links.py`
-into `scripts/` as `librarian_check_links.py` (one-file lychee wrapper),
-verified to run against `docs/**`. No JSON aggregation yet — just exit
-code 0/non-zero. This proves the deterministic-lint layer works on this
-repo before adding the custom checks (code citations, stale plans,
-etc.).
+Build `scripts/librarian.sh` as a thin orchestrator that runs every
+existing Stage 1 check in order and aggregates the exit code. Two
+checks today, more land incrementally. This gives a single entry
+point so users (and future cron) can run `scripts/librarian.sh`
+instead of remembering each individual checker.

docs/research/optimization_sequencing.md

@@ -8,7 +8,7 @@
 | --- | --- | --- |
 | **Model size growth** (hidden ≥ 1024 / layers ≥ 6) | `docs/plans/model_size_experiment.md` | 인프라 미설치 |
 | **Option B** (per-worker interleaved traversal) | plan 미작성 | 미시작 |
-| **AMP** trainer | `docs/plans/amp_trainer.md` (구현 됨, default off) | 모델 키운 후 재측정 |
+| **AMP** trainer | `docs/plans/archive/amp_trainer.md` (구현 됨, default off) | 모델 키운 후 재측정 |
 | **torch.compile** trainer | `docs/plans/torch_compile.md` | 모델 키운 후 재측정 |
 | **TensorRT** inference | plan 미작성 | 모델 키운 + eval dense 시점 |
 | **Option A re-enable** | 코드 있음 (default off) | 모델 키운 후 또는 Option B 후 |

scripts/librarian-ignore.txt

@@ -0,0 +1,23 @@
+# Ignore patterns for scripts/librarian_check_citations.py.
+#
+# One fnmatch glob per line. Citations matching any pattern are
+# silently skipped — use sparingly, only for citations that are
+# genuinely intentional (planned future files, design references)
+# rather than drift you can fix.
+#
+# Format examples:
+#   scripts/foo.sh                   # exact path
+#   configs/deep_cfr/model-*.yaml    # glob
+#   docs/research/*.md               # whole directory
+#
+# Comments after `#` are stripped per line. Blank lines ignored.
+
+# Future deliverables described in docs/plans/librarian.md
+scripts/librarian.sh
+
+# Future config + script described in docs/plans/model_size_experiment.md
+configs/deep_cfr/model-size-*.yaml
+scripts/run_model_size_experiment.sh
+
+# Future config described in docs/plans/torch_compile.md
+configs/deep_cfr/default_compile.yaml

scripts/librarian_check_citations.py

@@ -0,0 +1,161 @@
+"""Code citation checker for librarian Stage 1.
+
+Walks markdown files, extracts file:line citations from inline code
+spans (single backticks), and verifies each path exists and (if a line
+number is given) is within range.
+
+Inline code only — fenced code blocks are intentionally skipped to keep
+false positives down (snippets often contain string literals like
+"foo.py" that aren't real cross-references).
+
+Citations to external repos (paths whose first segment isn't one of
+this repo's tracked top-level dirs) are silently skipped.
+
+Usage:
+    uv run python scripts/librarian_check_citations.py
+"""
+
+from __future__ import annotations
+
+import fnmatch
+import re
+import sys
+from pathlib import Path
+
+EXCLUDED_DIRS = {
+    ".git",
+    ".mypy_cache",
+    ".pytest_cache",
+    ".ruff_cache",
+    ".venv",
+    "__pycache__",
+    "build",
+    "dist",
+    "node_modules",
+    "runs",
+    "target",
+    "tools",
+    "wheels",
+}
+
+ALLOWED_TOP = {"src", "docs", "tests", "configs", "scripts", "experiments"}
+
+INLINE_CODE = re.compile(r"`([^`\n]+)`")
+PATH_REF = re.compile(
+    r"([\w.-]+(?:/[\w.-]+)+\.(?:pyx|pxd|py|toml|yaml|yml|json|md|sh|rs|txt|c|h))"
+    r"(?::(\d+))?"
+)
+
+
+def _repo_root() -> Path:
+    current = Path(__file__).resolve()
+    for parent in current.parents:
+        if (parent / "pyproject.toml").is_file():
+            return parent
+    raise RuntimeError("pyproject.toml을 찾을 수 없어 repository root를 판정할 수 없습니다.")
+
+
+def _is_excluded(path: Path) -> bool:
+    return any(part in EXCLUDED_DIRS for part in path.parts)
+
+
+EXCLUDED_DOC_PREFIXES = (
+    Path("docs/archive"),
+    Path("docs/plans/archive"),
+)
+
+
+def _is_archive_doc(rel: Path) -> bool:
+    return any(prefix in rel.parents for prefix in EXCLUDED_DOC_PREFIXES)
+
+
+def _markdown_files(root: Path) -> list[Path]:
+    files: list[Path] = []
+    for path in root.rglob("*.md"):
+        rel = path.relative_to(root)
+        if _is_excluded(rel) or _is_archive_doc(rel):
+            continue
+        files.append(path)
+    return sorted(set(files))
+
+
+def _load_ignore_patterns(root: Path) -> list[str]:
+    ignore_file = root / "scripts" / "librarian-ignore.txt"
+    if not ignore_file.is_file():
+        return []
+    patterns: list[str] = []
+    for raw in ignore_file.read_text(encoding="utf-8").splitlines():
+        line = raw.split("#", 1)[0].strip()
+        if line:
+            patterns.append(line)
+    return patterns
+
+
+def _is_ignored(target: str, patterns: list[str]) -> bool:
+    return any(fnmatch.fnmatchcase(target, pat) for pat in patterns)
+
+
+def _check_citation(root: Path, target: str, line_num: int | None) -> str | None:
+    """Return error message if the citation is broken; None if OK or external."""
+    first = target.split("/", 1)[0]
+    if first not in ALLOWED_TOP:
+        return None
+
+    target_path = (root / target).resolve()
+    try:
+        target_path.relative_to(root.resolve())
+    except ValueError:
+        return None
+
+    if not target_path.is_file():
+        return f"file not found: {target}"
+
+    if line_num is not None:
+        with target_path.open(encoding="utf-8", errors="replace") as f:
+            actual_lines = sum(1 for _ in f)
+        if line_num > actual_lines:
+            return f"line {line_num} out of range (file has {actual_lines} lines)"
+
+    return None
+
+
+def main() -> int:
+    root = _repo_root()
+    files = _markdown_files(root)
+    if not files:
+        print("검사할 Markdown 파일이 없습니다.", file=sys.stderr)
+        return 1
+
+    ignore_patterns = _load_ignore_patterns(root)
+
+    errors: list[tuple[Path, int, str, int | None, str]] = []
+    for doc in files:
+        rel = doc.relative_to(root)
+        with doc.open(encoding="utf-8", errors="replace") as f:
+            for line_idx, line in enumerate(f, 1):
+                for span in INLINE_CODE.finditer(line):
+                    span_text = span.group(1)
+                    if "://" in span_text:
+                        continue
+                    for match in PATH_REF.finditer(span_text):
+                        target = match.group(1)
+                        line_num_str = match.group(2)
+                        line_num = int(line_num_str) if line_num_str else None
+                        if _is_ignored(target, ignore_patterns):
+                            continue
+                        err = _check_citation(root, target, line_num)
+                        if err:
+                            errors.append((rel, line_idx, target, line_num, err))
+
+    if not errors:
+        print("All code citations resolve.")
+        return 0
+
+    for rel, doc_line, target, line_num, err in errors:
+        cite = f"{target}:{line_num}" if line_num else target
+        print(f"{rel}:{doc_line}: `{cite}` — {err}")
+    return 1
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())