fix: reduce retry log noise during concurrent chunk processing

Addresses issue #362 - users were seeing hundreds of ERROR/WARNING logs
when processing large documents due to SurrealDB v2 transaction conflicts
during concurrent chunk embedding operations.

Changes:
- Upgraded to surreal-commands v1.3.0 which includes retry_log_level feature
- Increased retry attempts from 5 to 15 with max wait time 120s (from 30s)
  to handle deep queues during concurrent processing
- Set retry_log_level to "debug" in embed_chunk and process_source commands
- Changed repository.py RuntimeError logging from ERROR to DEBUG level
- Updated command exception handlers to log retries at DEBUG level
- Updated documentation to reflect retry strategy

This is a temporary workaround for SurrealDB v2.x transaction conflict
issues with SEARCH indexes. Settings can be reduced after migrating to
SurrealDB v3 which fixes the underlying concurrency issue.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

open_notebook/database/repository.py

@@ -74,8 +74,8 @@ async def repo_query(
                 raise RuntimeError(result)
             return result
         except RuntimeError as e:
-            # RuntimeError is raised for retriable transaction conflicts - log without stack trace
-            logger.error(str(e))
+            # RuntimeError is raised for retriable transaction conflicts - log at debug to avoid noise
+            logger.debug(str(e))
             raise
         except Exception as e:
             logger.exception(e)