refactor: split app orchestration and backend core modules

[Dimillian]

Summary

• split app-level orchestration out of src/App.tsx into dedicated bootstrap and orchestration modules
• decompose Settings into orchestration + section-state hooks + section container routing
• modularize daemon RPC routing into domain handlers under src-tauri/src/bin/codex_monitor_daemon/rpc/*
• split shared backend cores into module folders:
  • src-tauri/src/shared/git_ui_core/*
  • src-tauri/src/shared/workspaces_core/*
• split threads reducer into focused slices under src/features/threads/hooks/threadReducer/*
• add TS/Vite path aliases and rationalize imports in touched files
• add docs/codebase-map.md as a task-oriented navigation map
• slim AGENTS.md, keep core run/test commands inline, and link to docs/codebase-map.md

Dead Code / Cleanup

• removed intermediate/unwired artifacts from refactor iterations
• removed unused helper introduced during intermediate split (SettingsSectionPanels)
• reverted unrelated formatting-only Rust changes to keep the PR focused

Validation

• npm run typecheck
• npm run test
• cd src-tauri && cargo check
• targeted Rust tests:
  • cargo test --manifest-path src-tauri/Cargo.toml shared::git_ui_core::tests::
  • cargo test --manifest-path src-tauri/Cargo.toml shared::workspaces_core::helpers::tests
  • cargo test --manifest-path src-tauri/Cargo.toml rpc_

[Dimillian]

@codex review

[chatgpt-codex-connector]

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Reviewed commit: ca783e374b

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[Dimillian]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Keep it up!

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

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Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".