fix: resolve five P1 defects from the SDK review

- AgentRunner.run: offload to a worker-thread event loop when called
  from inside a running loop (Jupyter, FastAPI handlers) — mirrors
  pipeline._run_async; Runner.run_sync raised RuntimeError there.

- SQLiteStorage: create connections with check_same_thread=False so
  close() can actually close connections created by worker threads.
  Each thread still gets its own connection via threading.local; with
  the default True those closes raised ProgrammingError (silently
  swallowed) and leaked every worker connection.

- CloudBackend.query: non-streaming chat completions now use a 300s
  timeout and a single attempt. The default 30s ReadTimeout fired
  before generation finished and the retry loop re-billed the full
  server-side retrieval + generation up to three times. _request gains
  retries/timeout overrides; the exhausted-retry path also no longer
  sleeps before raising.

- MarkdownParser: content before the first heading (abstract/preamble)
  becomes a node instead of being silently dropped and unretrievable;
  a file with no headings at all yields a single document node instead
  of zero nodes (which pushed an empty page list into the pipeline).

- LegacyCloudAPI.is_retrieval_ready: API failures (revoked key, network
  down) now propagate as PageIndexAPIError instead of reading as
  "not ready", which turned polling loops into infinite loops.

Adds regression tests for each fix.

Claude-Session: https://claude.ai/code/session_01Kx5DgKbhK1N8autqXH8SmS

tests/test_cloud_backend.py

@@ -202,3 +202,20 @@ def test_query_stream_connect_failure_raises_instead_of_hanging(monkeypatch):
 
     with pytest.raises(CloudAPIError, match="request failed"):
         asyncio.run(_run())
+
+
+def test_query_uses_long_timeout_and_single_attempt(monkeypatch):
+    """Non-streaming chat completion is non-idempotent and slow: it must get
+    a long timeout and must NOT be retried (each retry re-bills the query)."""
+    backend = CloudBackend(api_key="pi-test")
+    calls = []
+
+    def fake_request(method, url, headers=None, **kwargs):
+        calls.append(kwargs)
+        raise cloud_mod.requests.ConnectionError("boom")
+
+    monkeypatch.setattr(cloud_mod.requests, "request", fake_request)
+    with pytest.raises(CloudAPIError):
+        backend.query("col", "q", doc_ids=["d1"])
+    assert len(calls) == 1
+    assert calls[0]["timeout"] == 300