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_markdown_parser.py

@@ -53,3 +53,21 @@ def test_parse_nodes_have_index(sample_md):
     result = parser.parse(sample_md)
     for node in result.nodes:
         assert node.index is not None
+
+
+def test_preamble_before_first_header_is_kept(tmp_path):
+    md = tmp_path / "pre.md"
+    md.write_text("Abstract: important preamble text.\n\n# Chapter 1\nBody.\n")
+    result = MarkdownParser().parse(str(md))
+    assert result.nodes[0].title == "pre"
+    assert "important preamble text" in result.nodes[0].content
+    assert result.nodes[1].title == "Chapter 1"
+
+
+def test_headerless_file_yields_single_node(tmp_path):
+    md = tmp_path / "plain.md"
+    md.write_text("Just some text.\nNo headings at all.\n")
+    result = MarkdownParser().parse(str(md))
+    assert len(result.nodes) == 1
+    assert result.nodes[0].title == "plain"
+    assert "No headings at all" in result.nodes[0].content