fix(sources): correct OpenAlex ID prefixing, citations endpoint, S2 rate-limit

Review-Gate findings:
- openalex: bare DOIs/arXiv IDs need doi:/arxiv: prefix (bare IDs 404);
  add _resolve_id(); fix fetch_citations to use referenced_works field
  instead of non-existent /works/{id}/references endpoint.
- semanticscholar: wait_fixed(1) was inter-retry only; add per-request
  monotonic rate-limiter (_rate_limit()) before each httpx call.
  Add _is_retryable() filter so 404s don't burn 5 retry slots.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

codex/sources/openalex.py

@@ -24,6 +24,20 @@ logger = logging.getLogger(__name__)
 _BASE = "https://api.openalex.org"
 
 
+def _resolve_id(id: str) -> str:
+    """Prefix a bare DOI or arXiv ID for the OpenAlex /works/ endpoint.
+
+    OpenAlex accepts: doi:<doi>, arxiv:<id>, W-IDs, or full https:// URLs.
+    Bare DOIs (starting with "10.") and bare arXiv IDs require a prefix.
+    """
+    s = id.strip()
+    if s.startswith(("W", "https://", "doi:", "arxiv:")):
+        return s
+    if s.startswith("10."):
+        return f"doi:{s}"
+    return f"arxiv:{s}"
+
+
 def _is_retryable(exc: BaseException) -> bool:
     """Return True for HTTP 429 / 5xx responses wrapped in httpx.HTTPStatusError."""
     if isinstance(exc, httpx.HTTPStatusError):
@@ -88,14 +102,15 @@ def fetch_paper(id: str) -> Paper | None:
     Parameters
     ----------
     id:
-        An arXiv ID (``"2301.07041"``) or a DOI (``"10.1145/…"``).
+        An arXiv ID (``"2301.07041"``), a DOI (``"10.1145/…"``),
+        or an OpenAlex W-ID (``"W2741809807"``).
 
     Returns
     -------
     Paper | None
         A populated Paper instance, or None on 404.
     """
-    url = f"{_BASE}/works/{id}"
+    url = f"{_BASE}/works/{_resolve_id(id)}"
     try:
         response = _get(url)
     except httpx.HTTPStatusError as exc:
@@ -109,17 +124,20 @@ def fetch_paper(id: str) -> Paper | None:
 def fetch_citations(openalex_id: str) -> list[Citation]:
     """Fetch the reference list for a paper as Citation objects.
 
+    Uses the ``referenced_works`` field from the work object — the
+    ``/works/{id}/references`` path is not a real OpenAlex endpoint.
+
     Parameters
     ----------
     openalex_id:
-        The OpenAlex work ID (``"https://openalex.org/W…"`` or short ``"W…"``).
+        The OpenAlex work ID (``"https://openalex.org/W…"`` or ``"W…"``).
 
     Returns
     -------
     list[Citation]
-        One Citation per referenced work.
+        One Citation per referenced work (OpenAlex W-ID as cited_id).
     """
-    url = f"{_BASE}/works/{openalex_id}/references"
+    url = f"{_BASE}/works/{_resolve_id(openalex_id)}"
     try:
         response = _get(url)
     except httpx.HTTPStatusError as exc:
@@ -127,10 +145,10 @@ def fetch_citations(openalex_id: str) -> list[Citation]:
             return []
         raise
 
-    results: list[dict[str, Any]] = response.json().get("results", [])
-    citations: list[Citation] = []
-    for ref in results:
-        cited_id: str = ref.get("doi") or ref.get("id") or ""
-        if cited_id:
-            citations.append(Citation(citing_id=openalex_id, cited_id=cited_id))
-    return citations
+    data: dict[str, Any] = response.json()
+    referenced_works: list[str] = data.get("referenced_works", [])
+    return [
+        Citation(citing_id=openalex_id, cited_id=cited_id)
+        for cited_id in referenced_works
+        if cited_id
+    ]