v0.99.0: Incremental AutoWiki refreshes, themed mermaid diagrams, AutoWiki search, and CLI stability fixes

New features

- Incremental AutoWiki refreshes - AutoWiki refreshes now only update changed pages for faster updates
- Themed mermaid diagram colors - Mermaid diagrams now render with per-element colors that match your current theme
- AutoWiki search and exports - AutoWiki now supports keyword search, skill browsing, and page exports (Factory App)

Bug fixes

- Theme background override - Fixed terminal theme background being overridden unexpectedly
- BYOK base URL switching - Fixed client connections not being refreshed after switching custom API base URLs
- Context model inheritance - Fixed context management not using the current session model
- Spec editor terminal handoff - Fixed spec editor not properly completing terminal handoff
- MCP auth cancellation - Fixed pending MCP authentication not being cancelled when closing the MCP panel
- Tool result display - Fixed a crash when tool results contain non-string values
- Custom model stability - Fixed custom model IDs changing unexpectedly between sessions
- Directory not found error - Directory not found errors now appear immediately when confirming a directory (Factory App)
- BYOK Rate Limits - BYOK users can now continue chatting when platform Rate Limits are reached (Factory App)
- Ghost tool calls - Fixed phantom tool calls appearing during message processing
- Chat input - Fixed various chat input issues (Factory App)
- Droid Computer terminal - Fixed terminal display issues when using Droid Computers (Factory App)
- Machine config modal - Fixed machine configuration modal not displaying correctly (Factory App)
- Reasoning and model selection - Fixed reasoning level and model selection issues (Factory App)