content.split("\n") yields a trailing empty element for any file ending in a
newline, inflating total by 1 and letting a start_line one past real EOF be
silently accepted instead of rejected. Mirrors the trailing-newline correction
default_file_chunker already applies, and matches the large-file path's
line-by-line count.
Fixes#388
* feat(codex): add authentication mode support with thread-safe logging
- Implement _CodexAuthConfig dataclass for resolved auth settings
- Add auth_mode parameter with auto/api_key/oauth options
- Separate API key and OAuth authentication flows
- Force specific login method based on auth mode
- Add explicit API key validation requirement
- Serialize concurrent logger initialization in thread lock
- Close logging handlers properly during cleanup
- Update default config with auth_mode presets for codex and codex_oauth
- Add comprehensive tests for authentication modes and concurrent logging
* feat(file_store): implement background embedding backfill and keyword index repair
- Add _after_embedding_backfill hook in FAISS local file store
- Schedule startup embedding repair without delaying component readiness
- Cancel and collect embedding backfill task during component shutdown
- Log progress at fixed percentage boundaries for long-running operations
- Process embedding backfill in configurable batch sizes with progress reporting
- Rebuild keyword index in bounded batches with detailed mismatch diagnostics
- Format stdlib logs consistently with QwenPaw console output using relative paths
- Run embedding backfill as background task that doesn't block component startup
- Add comprehensive tests for background embedding and keyword index repair scenarios
* fix(file-store): repair graph-chunk consistency on load
- Add _repair_graph_chunk_consistency method to detect and fix mismatched graph/chunk states
- Clear torn graph/chunk state when missing or orphaned chunks are detected
- Ensure keyword index sync handles empty chunks properly
- Add comprehensive tests for graph-chunk consistency scenarios
- Update test utilities to properly seed graph/chunk snapshots
- Increment version to 0.4.1.2
* feat(file_io): enhance list step response format and add comprehensive logging
- Format list output with bullet points for better readability
- Add explicit "No files found" message when directory is empty
- Include detailed timing information for file store startup phases
- Add logging for chunk loading, graph consistency checks, and keyword indexing
- Provide detailed metrics for embedding backfill operations
- Add comprehensive test coverage for empty directory scenarios
- Include batch processing statistics for embedding operations
* feat(logger): add QwenPaw logging integration with forwarding mechanism
- Introduce _ForwardToLoggerHandler to forward log records to target logger
- Add qwenpaw logger integration that forwards ReMe logs to QwenPaw handlers
- Maintain ReMe logger stability for modules that cache it at import time
- Enable QwenPaw handlers to take effect without ReMe reconfiguration
- Add comprehensive tests for stdlib forwarding to QwenPaw sinks
- Support explicit REME_DISABLE_LOGURU=false to keep original Loguru backend
- Preserve existing logging behavior when QwenPaw is not configured
* fix(file_store): serialize concurrent FAISS dump operations to prevent corruption
- Add asyncio lock to ensure only one FAISS dump operation runs at a time
- Generate unique temporary filenames using UUID tokens for atomic replacement
- Implement proper cleanup of temporary files in finally block
- Add comprehensive test to verify concurrent dumps are serialized
- Ensure atomic writes by replacing both index and idmap files together
- Prevent partial state writes during concurrent access scenarios
* docs: rename vault_dir to workspace_dir in documentation and examples
* refactor(extract): format long method call across multiple lines
* refactor(extract): format system prompt parameters for better readability
