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/storage/sqlite.py

@@ -16,7 +16,12 @@ class SQLiteStorage:
     def _get_conn(self) -> sqlite3.Connection:
         """Return a thread-local SQLite connection."""
         if not hasattr(self._local, "conn"):
-            conn = sqlite3.connect(str(self._db_path))
+            # Each thread gets its own connection (threading.local), so
+            # statements never race. check_same_thread=False exists solely so
+            # close() can close every tracked connection from whichever thread
+            # calls it — with the default True those closes raise
+            # ProgrammingError and the connections leak.
+            conn = sqlite3.connect(str(self._db_path), check_same_thread=False)
             conn.execute("PRAGMA journal_mode=WAL")
             conn.execute("PRAGMA foreign_keys=ON")
             self._local.conn = conn