Feat/webui refractor

[alcholiclg]

Change Summary

This PR refactors the agent runtime to improve responsiveness, replay fidelity, and live configuration synchronization.

• Adds non-blocking, interruptible LLM streaming, configurable OpenAI timeouts, and improved Anthropic thinking/tool support.
• Persists partial rounds, reasoning, errors, permission decisions, skill invocations, and execution timings for reliable session resume and replay.
• Adds live global/project skill discovery, mid-session catalog refresh, skill update notices, and bare or inline /skill expansion.
• Hardens tool and MCP management with enabled-flag support, targeted and idempotent re-indexing, degraded-tool handling, and permission call correlation.
• Improves managed-config environment expansion, workspace-isolated memory, Mem0 integration, and todo lock storage.
• Adds focused regression tests and updates dependency and CI coverage.

Related issue number

Checklist

• The pull request title is a good summary of the changes - it will be used in the changelog
• Unit tests for the changes exist
• Run pre-commit install and pre-commit run --all-files before git commit, and passed lint check.
• Documentation reflects the changes where applicable

[gemini-code-assist]

Caution

The consumer version of Gemini Code Assist on GitHub has been sunset. All code review activity has officially ceased.