chore: bump version to 0.4.1-alpha

Features:
- feat(docker): update development Docker Compose configuration and installation script (06a415a)
- feat(setup): enhance Dockerfile and installation script for improved project structure and environment handling (e6e80c7)
- feat(install): improve installation script and Docker integration (ffb63bb)
- feat(install): enhance Docker support in setup wizard (01b0d2e)
- feat(install): enhance interactive setup wizard for Docker execution (ce26651)
- feat(multi-chat-modal): enhance message handling and logging for tool calls (b641398)
- feat(services): enhance file conversion process and update dependencies (d94351c)
- feat(projects): implement project management CLI commands and sync service (d2c0169)
- feat(monitor): add knowledge folder auto-indexing watcher (d5d8c56)
- feat(config): update knowledge base path to user-facing location (a1d80f6)
- feat(services): integrate knowledge service and add health checks (da5bae1)
- feat(skills): add external knowledge agent skills (678f1c8)
- feat(cli): add knowledge management CLI commands (7f4d507)
- feat(mcp): add external knowledge MCP tools (bee0216)
- feat(rag): extend RAG system for external knowledge filtering (d762986)
- feat(knowledge): add core knowledge management services (c506783)
- feat(db): add knowledge collections schema migration (e431446)
- feat(knowledge): add external knowledge dependencies (dd3460f)
- feat(update-checker): Implement update checking functionality (8f5d242)
- feat(attachments): Add file upload support in FastAPI and enhance chat modal (bb8d45d)
- feat(tools): Add schema and prompt management tools to MCP (b32bcf0)
- feat(config): Enhance agentic retrieval settings with CRAG thresholds and knowledge refinement options (ff29079)
- feat(evaluation): Add agentic retrieval metrics tracking (c7070af)
- feat(ui): Add real-time progress indicators for agentic retrieval (c7cd0b6)
- feat(rag): integrate agentic retrieval into backend + MCP tool (0443ce2)
- feat(rag): add LangGraph agentic retrieval orchestrator (744a7ce)
- feat(rag): add agentic RAG building blocks (bb58d06)
- feat(migrations): Add discovered_articles table and update article_discoveries schema (03b4ecf)
- feat(release): Add release management functionality (eaec387)
- feat(discovery): Implement browser workflow support and async execution (1a963f0)
- feat(chat-modal): Add agent working state to chat input (13a23d3)
- feat(multi-chat-modal): Enhance message handling in chat modal (e490699)
- feat(skill-tools): Implement skill loading/unloading persistence and auto-follow-up (6128a25)
- feat(extraction): Enhance metadata extraction with detail page enrichment and meta tag support (dea06be)
- feat(attachments): Implement image attachment functionality in chat modal (32262a1)

Bug Fixes:
- fix(docker): update Dockerfile and installation script for microservices configuration (eb27a16)
- fix(install): update installation script and completion screen for microservices support (da1d220)
- fix(install): improve version resolution and Docker detection in install script (579f797)
- fix(tools): normalize authors consistently across all MCP tool files (12021a1)
- fix(modal): Remove redundant import of retrieval step functions in MultiChatModal (0602f9b)
- fix(monitor): replace stale healthcheck and fix config reload signatures (f4bab5d)
- fix(mcp): Add AgenticResearchQuestionMCPTool to MCP_TOOL_CLASSES (ed0feeb)
- fix: invalidate name/user cache on research question delete (eae2bde)
- fix: Correct type hint for ServiceManager constructor (0c22609)

Refactors:
- refactor(setup): enhance API key and deployment mode screens for improved configuration handling (9d8999e)
- refactor(docker): streamline Docker configuration and remove deprecated files (0e4c1ca)
- refactor(install): update installation script and completion screen for Thoth dev microservices (5b9fa35)
- refactor(setup): streamline Dockerfile and installation script for improved service management (fa31755)
- refactor(mcp-servers): Simplify endpoint construction and enhance tool listing (c139ecd)
- refactor(release): Enhance release script for interactive steps and changelog generation (42ae9bb)
- refactor: Enhance MCP server registration and management (38ec567)
- refactor(tests): Update text normalization test for casefold stability (3be9798)
- Refactor: Update Docker Compose and configuration paths (8efd6ed)

Documentation:
- docs(config): Add agentic retrieval settings to example config (f42131a)
- docs(config): Add agentic retrieval settings to example config (0355d46)

Chores:
- chore(docs): Update documentation and configuration for agentic retrieval (ea26d6f)

Other:
- Fix test: mock article elements for detail page extraction test (3a54225)

Author: acertainKnight

pyproject.toml

@@ -7,7 +7,7 @@ name = "thoth"
 description = "Thoth AI Research Agent - An autonomous system for academic research paper processing and knowledge management"
 readme = "README.md"
 requires-python = ">=3.12, <3.13"
-version = '0.4.0-alpha'
+version = '0.4.1-alpha'
 authors = [{name="Nick Hallmark", email="NHALLMARK3@BLOOMBERG.NET"}]
 
 dependencies = [