feat: Complete Skills and Multi-Agent system integration

- Integrate SkillsManager into Session with system prompt injection
- Add ThreadManager global singleton (init/get/try_get functions)
- Create SkillPicker widget for TUI with fuzzy search
- Add skills_bridge for TUI-engine integration
- Add comprehensive tests for ThreadManager (8 tests)
- Add tests for SkillPicker (3 tests)

Skills System:
- SkillsManager loads skills per cwd with caching
- Skills rendered in system prompt via progressive disclosure
-  detection and on-demand content loading

Multi-Agent System:
- ThreadManager with create/fork/switch/close operations
- ThreadEvent broadcasting for UI updates
- Thread state management with RwLock

Windows Sandbox (10 modules):
- winutil, env, cap, token, acl, audit
- dpapi, identity, sandbox_users, process

Author: Factory Bot

Cargo.lock

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+# SYNTHESE EXECUTIVE: Codex vs Cortex CLI
+
+## Verdict Global
+
+| Aspect | Codex | Cortex | Verdict |
+|--------|-------|--------|---------|
+| **Core Engine** | Focused, API-centric | Feature-rich, extensible | Cortex +features, Codex +polish |
+| **TUI** | Markdown streaming, backtrack | 120 FPS, multi-provider | Different strengths |
+| **Sandboxing** | Windows complet | Linux/macOS OK, Windows incomplet | **Codex gagne** |
+| **MCP** | OAuth, protocol 2025-06-18 | Basique, protocol 2024-11-05 | **Codex gagne** |
+| **Skills/Plugins** | SKILL.md, $mentions, AGENTS.md | Plugins dynamiques, hooks | Different paradigms |
+| **SDK** | TypeScript complet | Editeurs (nvim, zed, jetbrains) | Different focus |
+| **Distribution** | NPM avec binaires | Direct binary, self-update | Codex +accessible |
+| **GUI Desktop** | Absent | Tauri + SolidJS | **Cortex gagne** |
+
+---
+
+## TOP 10 FONCTIONNALITES MANQUANTES (Priorite Critique)
+
+| # | Fonctionnalite | Impact | Effort |
+|---|---------------|--------|--------|
+| 1 | **Windows Sandbox Complet** (ACL, env vars, audit) | Securite critique | Eleve |
+| 2 | **Skill Mentions ($skill_name)** | UX majeure | Moyen |
+| 3 | **AGENTS.md Hierarchique** | Personnalisation projet | Faible |
+| 4 | **OAuth 2.0 pour MCP** | Integration MCP servers | Moyen |
+| 5 | **Backtrack System (Undo)** | UX conversation | Moyen |
+| 6 | **Streaming Markdown** | UX visuelle | Moyen |
+| 7 | **File Search (@filename)** | Productivite | Moyen |
+| 8 | **Token Auto-Refresh** | Fiabilite | Faible |
+| 9 | **SDK TypeScript** | Ecosystem JS/TS | Eleve |
+| 10 | **exec-server MCP** | Interception syscall | Eleve |
+
+---
+
+## AVANTAGES UNIQUES DE CORTEX (A Conserver)
+
+1. **GUI Desktop** - Application Tauri complete
+2. **Multi-Agent System** - 5 agents built-in, Agent Factory
+3. **Plugins Dynamiques** - Architecture extensible
+4. **Hook System** - Interception d'evenements
+5. **SDKs Editeurs** - Neovim, Zed, JetBrains
+6. **mDNS Discovery** - Decouverte reseau
+7. **REST API** - Accessible universellement
+8. **Browser Automation** - Playwright integre
+9. **Image Generation** - DALL-E integre
+10. **Undo/Redo** - Historique complet
+
+---
+
+## ROADMAP RECOMMANDEE
+
+### Phase 1: Securite (Semaines 1-4)
+- [ ] Windows Sandbox complet (ACL, env vars)
+- [ ] Token auto-refresh
+- [ ] SSRF protection renforcee
+
+### Phase 2: UX Core (Semaines 5-8)
+- [ ] Skill mentions ($skill_name)
+- [ ] AGENTS.md hierarchique
+- [ ] Backtrack system (Esc-Esc-Enter)
+- [ ] Streaming markdown
+
+### Phase 3: Integrations (Semaines 9-12)
+- [ ] OAuth 2.0 pour MCP
+- [ ] Protocol MCP 2025-06-18
+- [ ] File search (@filename)
+- [ ] exec-server MCP
+
+### Phase 4: Ecosystem (Semaines 13-16)
+- [ ] SDK TypeScript
+- [ ] Distribution NPM
+- [ ] VS Code extension
+
+---
+
+## FICHIERS DE CE DOSSIER
+
+1. `00-SYNTHESE-EXECUTIVE.md` - Ce fichier
+2. `01-CORE-ENGINE-GAPS.md` - Fonctionnalites core manquantes
+3. `02-TUI-GAPS.md` - Fonctionnalites TUI manquantes
+4. `03-SANDBOX-GAPS.md` - Gaps sandboxing (CRITIQUE)
+5. `04-MCP-GAPS.md` - Gaps MCP
+6. `05-SKILLS-GAPS.md` - Skills vs Plugins
+7. `06-SDK-GAPS.md` - SDKs manquants
+8. `07-AUTH-GAPS.md` - Authentification
+9. `08-FULL-FEATURE-LIST.md` - Liste complete des ameliorations

comparaisons-ameliorations/00-SYNTHESE-EXECUTIVE.md

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+# Core Engine: Fonctionnalites Manquantes
+
+## Fonctionnalites Presentes dans Codex mais ABSENTES dans Cortex
+
+### Critique
+
+| Fonctionnalite | Description | Fichier Codex | Impact |
+|---------------|-------------|---------------|--------|
+| **ExecPolicy System** | Politique d'approbation basee sur regles `.rules` | `exec_policy.rs` (1284 lignes) | Securite |
+| **ThreadManager** | Gestion multi-thread/conversation avec broadcasting | `thread_manager.rs` | Architecture |
+| **Unified Exec (ConPTY)** | Terminal PTY avec allocation ConPTY | `unified_exec/` | Windows support |
+| **Remote Compaction** | Compaction cote serveur via API | `compact_remote.rs` | Performance |
+| **Agent Control** | `AgentControl`, `AgentStatus`, agents hierarchiques | `agent/` | Multi-agent |
+
+### Haute Priorite
+
+| Fonctionnalite | Description | Fichier Codex |
+|---------------|-------------|---------------|
+| **Collaboration Modes** | `wait_for_input`, modes collaboratifs | `collab.rs` (42KB) |
+| **MCP Resources** | Templates de ressources, lecture MCP | `handlers/mcp_resource.rs` (25KB) |
+| **Request User Input** | Outil pour questions mid-turn | `handlers/request_user_input.rs` |
+| **Models Manager** | Listing modeles, presets, providers | `models_manager/` |
+| **Turn Diff Tracker** | Tracking changements fichiers par turn | `turn_diff_tracker.rs` (31KB) |
+| **Shell Snapshot** | Capture/restore etat shell | `shell_snapshot.rs` (25KB) |
+| **Environment Context** | Info riche OS/shell/user | `environment_context.rs` |
+| **Connectors** | Integrations services externes | `connectors.rs` |
+
+### Moyenne Priorite
+
+| Fonctionnalite | Description |
+|---------------|-------------|
+| **User Notification** | Systeme d'alertes utilisateur |
+| **Codex Apps MCP** | `codex_apps_mcp` server pour ChatGPT |
+| **Test Sync Tool** | Utilitaire synchronisation tests |
+| **Plan Tool (different)** | Implementation differente |
+
+## Differences d'Implementation Importantes
+
+### Architecture Session
+
+| Aspect | Cortex | Codex |
+|--------|--------|-------|
+| Orchestrateur principal | `Session` (1800 lignes) | `Codex` (5000+ lignes) |
+| Channels | `async_channel` (unbounded) | `async_channel` + `watch` |
+| Cancellation | `AtomicBool` flag | `CancellationToken` (tokio-util) |
+| Fork/Resume | Methodes directes | Via `ThreadManager` |
+
+### Execution d'Outils
+
+| Aspect | Cortex | Codex |
+|--------|--------|-------|
+| Shell tool | Local shell simple | Unified exec avec ConPTY |
+| Approval flow | In-session pending | `ExecPolicyManager` avec rules |
+| Streaming output | `ToolOutputChunk` enum | `StdoutStream` |
+| Parallel execution | Sequential en boucle | `ToolCallRuntime` parallel |
+
+### Authentification
+
+| Aspect | Cortex | Codex |
+|--------|--------|-------|
+| Storage | OS keyring + encrypted file | `AuthDotJson` + storage backend |
+| Token refresh | Manuel | Auto-refresh avec intervalle |
+| ChatGPT auth | Partiel | Full `AuthMode::ChatGPT` |
+| API key handling | `SecureApiKey` avec zeroization | Plain string avec masking |
+
+## Recommandations d'Implementation
+
+### 1. ExecPolicy System
+```rust
+// Ajouter cortex-execpolicy/src/rules.rs
+pub struct PrefixRule {
+    pub pattern: PrefixPattern,
+    pub decision: Decision,  // Allow | Deny | Ask
+    pub justification: Option<String>,
+}
+```
+
+### 2. ThreadManager
+```rust
+// Ajouter cortex-engine/src/thread_manager.rs
+pub struct ThreadManager {
+    threads: RwLock<HashMap<ThreadId, Arc<Thread>>>,
+    created_tx: broadcast::Sender<ThreadId>,
+}
+```
+
+### 3. Unified Exec
+- Porter `codex-rs/core/src/unified_exec/` vers Cortex
+- Implementer ConPTY pour Windows
+- Ajouter `spawn_pty_process()`