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

pageindex/cloud_api.py

@@ -85,11 +85,15 @@ class LegacyCloudAPI:
         return response.json()
 
     def is_retrieval_ready(self, doc_id: str) -> bool:
-        try:
-            result = self.get_tree(doc_id)
-            return result.get("retrieval_ready", False)
-        except PageIndexAPIError:
-            return False
+        """Return whether retrieval is ready for ``doc_id``.
+
+        API failures (revoked key, network down, unknown doc) propagate as
+        PageIndexAPIError instead of reading as "not ready" — swallowing them
+        turned ``while not is_retrieval_ready(...)`` polling loops into
+        infinite loops.
+        """
+        result = self.get_tree(doc_id)
+        return result.get("retrieval_ready", False)
 
     def submit_query(self, doc_id: str, query: str, thinking: bool = False) -> dict[str, Any]:
         payload = {