refactor(server,modules,utils,frontend): split oversized modules into packages and fix regressions
- Split server/chat.py, server/status.py, server/tasks.py into sub-packages
- Split utils/context_manager.py, utils/conversation_manager.py into mixin packages
- Split modules/file_manager.py, persistent_terminal.py, terminal_ops.py, mcp_client_manager.py into packages
- Split core/main_terminal_parts/context.py into base + mixins
- Split static/src/app/methods/{ui,message,upload,taskPolling,conversation} into sub-modules
- Fix flattened method exports, dynamic import paths, missing cross-module imports
- Add missing permission/network/execution mode constants and _PERMISSION_MODE_LABEL
- Update AGENTS.md, CLAUDE.md and project memories to reflect new structure
JOJO
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