diff --git a/README.md b/README.md
index 43a9c78..1d4b1ff 100644
--- a/README.md
+++ b/README.md
@@ -1,379 +1,250 @@
-# Zesdex
+# Zesdex — Autonomous AI Coding Agent
 
-> Autonomous AI coding agent in a terminal-based TUI.
+Zesdex is an autonomous AI coding agent with a Terminal UI (TUI). It acts as an
+OpenAI/Anthropic-compatible LLM client wrapped in a tool-use harness with **37
+built-in tools** — file operations, git, shell execution, LSP integration, MCP,
+subagent orchestration, and more.
 
-Zesdex is a Rust-powered AI assistant that operates directly in your terminal via a rich TUI interface. It combines large language model intelligence with a comprehensive set of tools to explore, understand, and modify codebases autonomously — with built-in guardrails at every layer.
+```
+┌──────────────────────────────────────────────────────────────┐
+│                       Mode Selector                            │
+│  TUI (default) ─── Daemon ─── Attach ─── API ─── WS/gRPC/Web │
+└──────────────────────────────────────────────────────────────┘
+```
 
 ---
 
-## Features
+## Quick Start
 
-### Core
+```bash
+# Run the TUI (default mode)
+cargo run
 
-- **TUI Interface** — Full-screen terminal UI with chat panel, input bar, and status bar built with [ratatui](https://github.com/ratatui-org/ratatui) and [crossterm](https://github.com/crossterm-rs/crossterm).
-- **Daemon Architecture** — Run as a background daemon with client attach/detach via Unix domain sockets. The daemon processes state; clients only render.
-- **IPC Protocol** — Bidirectional state synchronization between daemon and client processes with diff-based updates.
-- **Provider Agnostic** — Configurable AI model providers with dynamic model selection, per-role temperature/token limits, and API key management.
+# Run the REST API server
+cargo run -- --api --api-port 8080
 
-### Tool System (37 built-in tools)
+# Run in daemon mode (background + IPC)
+cargo run -- --daemon
 
-| Category | Tools |
-|----------|-------|
-| **Filesystem** | `read`, `write`, `edit`, `delete` |
-| **Search** | `grep` (recursive text), `glob` (file patterns) |
-| **Shell** | `bash`, `bash_output`, `bash_kill` |
-| **Git** | `git_operator`, `git_worktree`, `git_cred` |
-| **Memory** | `remember`, `recall`, `forget` |
-| **Planning** | `plan_enter`, `plan_ready`, `seqthink` |
-| **Workflow** | `workflow_run`, `note_finding`, `read_findings`, `hive_mind` |
-| **Utility** | `cd`, `dir_list`, `dir_cache_update`, `pong`, `todowrite`, `todofinish` |
-| **Agent** | `spawn_agents`, `spawn_pipeline` |
-| **LSP** | `lsp_connect`, `lsp_diagnostics`, `lsp_hover`, `lsp_completion`, `lsp_definition`, `lsp_references`, `lsp_disconnect` |
+# Attach TUI to a running daemon session
+cargo run -- --attach <session-id>
 
-### Intelligence
+# Seed initial data (first run)
+cargo run --bin bootstrap
+```
 
-- **Hive-Mind Orchestration** — Autonomous agent orchestration modeled as a distributed machine intelligence (à la Stellaris). The Core Intelligence (main agent) compiles a cognitive cycle plan per task — an ordered list of cycles, each a set of anonymous processing nodes that run in parallel. Every node carries only a directive (what to do) and an access tier (`read`/`write`/`full`); cycle count and nodes-per-cycle are decided per task, not fixed. Every node's output merges into a shared collective state the instant it completes, and a final synthesis node reconciles it into one consensus. Every convergence is written to `docs/runs/*.md`. Manual entry point: the `hive_mind` tool.
+### Prerequisites
 
-- **Workflow Engine** — Orchestrate complex multi-step tasks with parallel sub-agents, pipelines, and phased execution. Spawn independent workers that share findings in real-time.
-- **Self-Learning** — Persistent memory system that stores lessons, references, and project knowledge across sessions. Memories include provenance tracking, lifecycle management, and scope isolation.
-- **Self-Review** — Review subagents trigger automatically after each code edit (inline) and at turn completion (background). Three types: code quality, architecture, and security.
-- **Self-Healing** — On build/test failures, spawns a sub-agent with the error context to autonomously fix issues before reporting them to the user.
-- **MCP Support** — [Model Context Protocol](https://modelcontextprotocol.io/) integration for connecting to external AI tool servers.
-- **Sequential Thinking** — Chain-of-thought reasoning tool for step-by-step problem decomposition.
-- **Session Locking** — Prevents multiple processes from operating on the same session directory.
+- **Rust** 1.81+ (edition 2021)
+- **Linux** or **macOS** (Unix domain sockets required for daemon mode)
+- An **API key** for an OpenAI/Anthropic-compatible LLM provider (set via
+  settings or environment variable)
 
-### Session Management
+---
 
-- Multiple concurrent sessions with history, rewind, and transcript persistence.
-- Per-session edit logs with full change tracking.
-- Session archival and summary generation.
+## Modes
+
+| Flag | Mode | Description |
+|------|------|-------------|
+| *(none)* | **TUI** | Full terminal UI with chat, overlays, and agent loop in one process |
+| `--daemon` | **Daemon** | Background daemon with IPC socket; clients attach separately |
+| `--attach <id>` | **Attach** | Connect TUI to an existing daemon session via Unix socket |
+| `--api` | **REST API** | HTTP server with session management and chat endpoints |
+| `--ws` | **WebSocket** | WebSocket server for real-time communication |
+| `--grpc` | **gRPC** | gRPC server for programmatic access |
+| `--web` | **Web** | Serves the web frontend |
+| `--api-port`, `--ws-port`, `--grpc-port`, `--web-port` | *(ports)* | Configure server ports (defaults: 8080, 8081, 50051, 3000) |
 
 ---
 
 ## Architecture
 
+### Clean Architecture Layering
+
 ```
-src/
-├── main.rs                    # Entry point: single-process, daemon, or attach mode
-├── resources.rs               # Embedded resources (help text, system prompts)
-├── app/
-│   ├── state/                 # AppStateRest — immutable-rest state model
-│   │   ├── rest.rs            # Core state struct
-│   │   ├── types.rs           # Overlay, Toast, Origin enums
-│   │   ├── snapshot.rs        # State snapshots for IPC
-│   │   ├── diff.rs            # Diff-based state synchronization
-│   │   ├── runtime.rs         # Runtime state mutations
-│   │   └── misc.rs            # DirCache and miscellaneous state helpers
-│   ├── runtime/               # Action dispatch and event loop
-│   │   ├── actions/           # Action enum and apply_action reducer
-│   │   ├── stream/            # LLM streaming and tool execution
-│   │   │   └── tools/         # Tool harness integration
-│   │   │   └── turn.rs        # Turn orchestration
-│   │   ├── event_loop/        # Main event loop and shortsend
-│   │   ├── commands.rs        # Slash command dispatch
-│   │   └── shortsend.rs       # Short-lived async send helper
-│   ├── mode/                  # UI modes and overlays (13 modes)
-│   │   ├── bash.rs            # Bash panel mode
-│   │   ├── editor.rs          # Multi-line editor mode
-│   │   ├── effort.rs          # Effort level selector
-│   │   ├── help.rs            # Help overlay
-│   │   ├── key_input.rs       # Raw key input mode
-│   │   ├── learning.rs        # Lesson management overlay
-│   │   ├── loading.rs         # Loading spinner overlay
-│   │   ├── mcp.rs             # MCP server management
-│   │   ├── quit_confirm.rs    # Quit confirmation dialog
-│   │   ├── rewind.rs          # Session rewind mode
-│   │   ├── settings.rs        # Settings panel
-│   │   ├── todo.rs            # Task list overlay
-│   │   └── workflow.rs        # Workflow visualization
-│   ├── harness.rs             # Tool harness for agent execution
-│   ├── workflow/              # Workflow engine
-│   │   ├── script.rs          # Workflow script DSL
-│   │   ├── engine.rs          # Workflow executor
-│   │   ├── hive_mind.rs       # Hive-mind orchestrator
-│   │   └── docs.rs            # Deterministic docs/runs/*.md writer
-│   ├── mcp/                   # MCP client manager
-│   │   └── manager.rs         # MCP server lifecycle and tool exposure
-│   ├── subagent/              # Sub-agent management
-│   │   ├── spawn.rs           # AgentDefinition and spawning
-│   │   ├── engine.rs          # Sub-agent event loop
-│   │   ├── context.rs         # Context construction for sub-agents
-│   │   └── event.rs           # Progress event types
-│   ├── bgbash/                # Background bash job management
-│   │   ├── job.rs             # Background job handle
-│   │   └── control.rs         # Bash control (bg/fg/kill)
-│   ├── lsp/                   # LSP client management
-│   │   ├── client.rs          # LSP client connection wrapper
-│   │   └── provisioner.rs     # Auto-provisioning of LSP servers
-│   └── review/                # Self-review quality system
-├── controller/
-│   ├── input.rs               # Key event → Action mapping
-│   └── command.rs             # Slash command parser
-├── dto/
-│   ├── chat/                  # Message, ToolCall, Role types
-│   │   ├── message.rs         # Chat message types
-│   │   ├── tool.rs            # Tool call/result types
-│   │   └── mod.rs
-│   └── provider/              # AI provider request/response/usage types
-│       ├── request.rs         # Provider request schema
-│       ├── response.rs        # Provider response schema
-│       └── usage.rs           # Token usage tracking
-├── ipc/
-│   ├── protocol.rs            # ClientRequest, DaemonFrame, StatePayload
-│   ├── server.rs              # Unix socket server
-│   ├── client.rs              # Unix socket client
-│   ├── conn.rs                # Framed connection
-│   ├── frame.rs               # Length-prefixed frame encoding
-│   ├── snapshot.rs            # State snapshot serialization
-│   └── diff.rs                # Binary diff for state sync
-├── model/
-│   ├── store.rs               # File-based storage (~/.config/zesdex/)
-│   ├── session.rs             # Session CRUD and listing
-│   ├── settings.rs            # User settings (provider, model, tokens)
-│   ├── app_config.rs          # Provider definitions and model roles
-│   ├── memory.rs              # Persistent memory with frontmatter
-│   ├── editlog.rs             # Edit history tracking
-│   ├── msglog/                # Message log (SQLite-backed)
-│   │   ├── schema.rs          # SQLite schema
-│   │   ├── query.rs           # Query helpers
-│   │   ├── blobs.rs           # Large blob storage
-│   │   └── summary.rs         # Session summarization
-│   ├── agent_def/             # Agent definitions (builtin, global, session)
-│   │   ├── builtin.rs         # Built-in agent profiles
-│   │   ├── global.rs          # Global agent config
-│   │   └── session.rs         # Per-session agent config
-│   ├── conversation.rs        # Conversation helpers
-│   └── session_lock.rs        # Flock-based session locking
-├── service/
-│   ├── provider.rs            # AI provider abstraction
-│   └── oauth/                 # OAuth PKCE flow with loopback server
-│       ├── loopback.rs        # Local HTTP server for OAuth redirect
-│       ├── manager.rs         # OAuth token manager
-│       ├── pkce.rs            # PKCE code challenge/verifier
-│       └── mod.rs
-├── tool/                      # 34 tool implementations
-│   ├── fs/                    # read, write, edit, delete
-│   │   ├── read.rs
-│   │   ├── write.rs
-│   │   ├── edit.rs
-│   │   ├── delete.rs
-│   │   └── helpers.rs         # Path resolution and validation
-│   ├── search.rs              # grep, glob
-│   ├── shell.rs               # bash
-│   ├── bash_tools.rs          # bash_output, bash_kill
-│   ├── git_operator.rs        # git operations
-│   ├── git_worktree.rs        # git worktree management
-│   ├── git_cred.rs            # git credential store/get/erase
-│   ├── memory/                # remember, forget, recall
-│   │   ├── remember.rs
-│   │   ├── forget.rs
-│   │   └── recall.rs
-│   ├── plan.rs                # plan_enter, plan_ready
-│   ├── seqthink.rs            # Sequential thinking
-│   ├── workflow.rs            # workflow_run, note_finding
-│   ├── utility/               # cd, dir_list, dir_cache_update, pong, todowrite, todofinish
-│   │   ├── cd.rs
-│   │   ├── dir_list.rs
-│   │   ├── dir_cache_update.rs
-│   │   ├── pong.rs
-│   │   ├── todowrite.rs
-│   │   └── todofinish.rs
-│   ├── lsp/                   # LSP tools (connect, diagnostics, hover, etc.)
-│   │   └── mod.rs
-│   └── shell_filter/          # Shell output filtering (credentials, git)
-│       ├── credentials.rs
-│       ├── git.rs
-│       └── mod.rs
-└── view/                      # TUI rendering
-    ├── chat.rs                # Chat transcript with markdown
-    ├── markdown.rs            # Markdown → ratatui spans
-    ├── status.rs              # Status bar
-    ├── theme.rs               # Color scheme
-    └── workflow.rs            # Workflow visualization
+apps/
+├── domain/          # Pure entities, value objects, repository/service traits
+│                    # Zero framework deps — only serde + chrono + uuid
+├── application/     # Use-case services (auth, sessions, conversations, memory)
+│                    # Depends only on domain-layer trait interfaces
+├── infrastructure/  # All I/O: LLM client, IPC, persistence, LSP, MCP, tools
+│                    # Implements domain/application port interfaces
+└── interfaces/      # Entry points
+    ├── tui/         # Ratatui terminal UI
+    ├── api/         # Axum REST API
+    ├── daemon/      # Unix socket daemon + client
+    ├── ws/          # WebSocket server
+    ├── grpc/        # gRPC server
+    └── web/         # Web frontend (static file server)
 ```
 
----
+### Tool System
 
-## Usage
+37 tools across 9 categories:
 
-```bash
-# Run in single-process mode (default)
-zesdex
+| Category | Tools |
+|----------|-------|
+| **File System** | `read`, `write`, `edit`, `delete`, `dir_list`, `dir_cache_update` |
+| **Shell** | `bash`, `bash_interactive`, `bash_kill`, `bash_output` |
+| **Git** | `git_operator`, `git_cred`, `git_worktree` |
+| **Search** | `search`, `grep`, `glob`, `semantic_search` |
+| **LSP** | `lsp_connect`, `lsp_hover`, `lsp_completion`, `lsp_definition`, `lsp_references`, `lsp_diagnostics`, `lsp_disconnect` |
+| **Memory** | `remember`, `recall`, `forget` |
+| **Workflow** | `spawn_agents`, `spawn_pipeline`, `plan`, `sequential_think`, `hive_mind` |
+| **Utility** | `todo_write`, `todo_finish`, `pong`, `cd` |
+| **Background** | Background bash jobs with `cancel/status/list` |
 
-# Run as a background daemon
-zesdex --daemon
-
-# Attach to a running daemon session
-zesdex --attach <session-id>
-
-# Set log level
-RUST_LOG=debug zesdex
-```
-
-### Key Bindings
-
-| Binding | Action |
-|---------|--------|
-| `Ctrl+Q` | Quit |
-| `Ctrl+H` | Help overlay |
-| `Ctrl+P` | Settings overlay |
-| `Ctrl+B` | Bash panel |
-| `Ctrl+S` | Session hub |
-| `Ctrl+T` | Task list |
-| `Ctrl+W` | Workflow view |
-| `Ctrl+K` | Key input mode |
-| `Esc` | Cancel / back |
-| `Tab` | Autocomplete |
-| `↑/↓` | History / navigation |
-| `Scroll` | Mouse scroll in chat |
-
-### Slash Commands
-
-| Command | Description |
-|---------|-------------|
-| `/help` | Show help |
-| `/clear` | Clear transcript |
-| `/model` | Select AI model provider |
-| `/workflow` | Open the workflow panel |
-| `/workflow run <script>` | Run a JSON-encoded workflow script |
-| `/mcp` | Open MCP server manager |
-| `/mcp add <name> <command>` | Add an MCP server |
-| `/login [provider]` | Authenticate with a provider |
-| `/edit [path]` | Open a file/dir in the external editor |
-| `/compact` | Compact the conversation transcript |
-| `/lesson` | Interactive lesson/memory review |
-| `/quit` | Exit application |
-| `Any text` | Sent to the AI assistant as a prompt |
-
----
-
-## Configuration
-
-All configuration lives in `~/.config/zesdex/` (or platform equivalent via the `dirs` crate).
-
-| File | Purpose |
-|------|---------|
-| `settings.json` | Provider selection, model, temperature, max tokens, review settings, workflow concurrency |
-| `app_config.json` | AI provider definitions (name, API base URL, auth type, default model) |
-| `memory/` | Persistent lesson and reference storage (Markdown with YAML frontmatter) |
-| `sessions/` | Per-session transcripts, edit logs, and activity data |
-| `run/` | Unix domain sockets for daemon mode |
-
-### Provider Configuration
-
-Providers are defined in `app_config.json`:
-
-```json
-{
-  "providers": {
-    "my-provider": {
-      "api_base": "https://api.example.com/v1",
-      "api_key_env": "MY_API_KEY",
-      "default_model": "model-name"
-    }
-  },
-  "model_roles": {
-    "default": {
-      "provider": "my-provider",
-      "model": "model-name",
-      "max_tokens": 8192,
-      "temperature": 0.7
-    }
-  },
-  "default_provider": "my-provider",
-  "default_model": "model-name"
+Each tool implements the `Tool` trait:
+```rust
+pub trait Tool: Send + Sync {
+    fn name(&self) -> &'static str;
+    fn description(&self) -> &'static str;
+    fn parameters(&self) -> Value;
+    fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String>;
 }
 ```
 
-### Settings
+### Hive Mind Orchestration
 
-Key settings in `settings.json`:
+The multi-agent orchestration system compiles a **cognitive cycle plan** per
+task — ordered cycles of parallel processing nodes. Each node has a directive
+and an **access tier** (`read` / `write` / `full`). Node outputs merge into a
+shared collective state in real time, and a final **consensus synthesis**
+produces the unified result.
 
-| Setting | Default | Description |
-|---------|---------|-------------|
-| `review_enabled` | `true` | Enable self-review after tool execution |
-| `review_max_lessons_per_run` | `5` | Max lessons loaded per review cycle |
-| `adaptive_review_max_skip` | `3` | Consecutive passes before skipping review |
-| `verify_command` | `null` | Optional command to verify changes |
-| `workflow_max_concurrency` | `5` | Max parallel sub-agents in workflows |
-| `session_archive_enabled` | `true` | Auto-archive completed sessions |
+- **Auto-trigger**: Complex requests automatically use the hive mind
+- **Manual entry**: The `hive_mind` tool lets the LLM specify cycles explicitly
+- **Live progress**: TUI panel shows each node's status and current tool
+- **Guaranteed docs**: Every convergence writes to `docs/runs/`
+
+### IPC Protocol (Daemon Mode)
+
+```
+┌──────────┐   Unix socket    ┌──────────┐
+│  Client   │ ◄──────────────► │  Daemon  │
+│  (TUI)    │   length-prefixed│          │
+└──────────┘   serde_json      └──────────┘
+
+Frame format: [4-byte BE length][JSON payload]
+```
+
+The daemon holds `AppStateRest` and drives the agent loop. Clients are stateless
+renderers that receive full state snapshots after each action.
 
 ---
 
-## Installation
+## Built-in Features
 
-### Prerequisites
+| Feature | Description |
+|---------|-------------|
+| **LLM Provider** | OpenAI/Anthropic-compatible API (streaming + non-streaming) with automatic retry and fallback |
+| **Tool Harness** | Safety-gated tool execution with graduated review checks |
+| **Subagents** | Auto-inline review, background test-gen, arch-review, security-review |
+| **OAuth 2.0** | PKCE flow for LLM provider authentication |
+| **MCP** | Model Context Protocol server management (stdio + HTTP transport) |
+| **LSP** | Language Server Protocol integration (completion, hover, diagnostics, references) |
+| **Session Mgmt** | SQLite-persisted sessions with lock-based concurrency control |
+| **Memory** | File-based memory system with frontmatter metadata |
+| **Edit Log** | Append-only edit history with configurable retention |
+| **Rate Limiting** | Sliding-window per-client rate limiter |
+| **JWT Auth** | HS256 JWT access/refresh tokens (API mode) |
+| **Password Auth** | Argon2 password hashing with pepper |
+| **OAuth Loopback** | Localhost HTTP server for OAuth redirect capture |
+| **Background Jobs** | Long-running shell jobs with cancellation and output collection |
+| **Settings** | JSON-persisted settings with hot-reload |
 
-- **Rust** 2021 edition toolchain ([rustup](https://rustup.rs/))
+---
 
-### Build from Source
+## TUI Overlays
+
+16 overlays accessible from the terminal UI:
+
+| Overlay | Purpose |
+|---------|---------|
+| Chat Input | Main input bar with autocomplete |
+| Bash Panel | Interactive shell panel |
+| File Editor | Built-in file editor |
+| Effort Selector | LLM reasoning effort selector |
+| Help | Keybindings reference |
+| Key Input | Custom key binding configuration |
+| Learning | Lesson viewer |
+| Loading | Generating spinner |
+| MCP Manager | MCP server management |
+| Model Selector | LLM model picker |
+| Quit Confirm | Exit confirmation dialog |
+| Rewind | Message/history rewind |
+| Settings | Settings panel |
+| Todo | Task/TODO list |
+| Usage | Token usage statistics |
+| Workflow | Hive-mind node progress |
+
+---
+
+## Data & Persistence
+
+All data lives under the platform's data directory (`~/.local/share/zesdex/`):
 
-```bash
-git clone <repository-url>
-cd zesdex
-cargo build --release
-./target/release/zesdex
 ```
-
+~/.local/share/zesdex/
+├── settings.json           # User settings (provider, model, keys)
+├── app_config.json         # Provider definitions (endpoints, env vars)
+├── sessions/               # Chat sessions (one subdirectory per session)
+│   └── <uuid>/
+│       ├── session.json    # Session metadata
+│       ├── messages.jsonl  # Message log
+│       └── .lock           # Session lock file
+└── memories/               # Memory files with frontmatter metadata
+    └── *.md
+```
 
 ---
 
 ## Development
 
-### Commit Convention
+```bash
+# Build all crates
+cargo build
 
-Project ini menggunakan **Conventional Commits** untuk otomatis menentukan versi rilis (melalui semantic-release).
+# Run all unit tests (8 tests across 11 crates)
+cargo test
 
-Format:
-```
-<type>(<scope>): <description>
+# Run clippy linting
+cargo clippy --all-targets
 
-[optional body]
-
-[optional footer]
+# Run with verbose logging
+RUST_LOG=debug cargo run
 ```
 
-**`<type>` — menentukan bump version:**
+### Workspace Crates
 
-| Type        | Bump    | Keterangan                                |
-|-------------|---------|-------------------------------------------|
-| `feat`      | minor   | Fitur baru                                |
-| `fix`       | patch   | Perbaikan bug                             |
-| `chore`     | patch   | Tugas maintenance, refactor ringan        |
-| `docs`      | patch   | Perubahan dokumentasi                     |
-| `refactor`  | patch   | Refactor kode (tanpa perubahan fungsional)|
-| `test`      | patch   | Penambahan atau perbaikan test            |
-| `style`     | patch   | Perubahan formatting, whitespace, dll     |
-| `perf`      | patch   | Optimasi performa                         |
-| `ci`        | patch   | Perubahan CI/CD                           |
+| Crate | Path | Layer |
+|-------|------|-------|
+| `zesdex-domain` | `apps/domain/` | Pure domain entities & traits |
+| `zesdex-application` | `apps/application/` | Use-case services |
+| `zesdex-infrastructure` | `apps/infrastructure/` | All I/O & tool implementations |
+| `zesdex-tui` | `apps/interfaces/tui/` | Ratatui terminal interface |
+| `zesdex-api` | `apps/interfaces/api/` | Axum REST API |
+| `zesdex-daemon` | `apps/interfaces/daemon/` | Unix socket daemon |
+| `zesdex-ws` | `apps/interfaces/ws/` | WebSocket server |
+| `zesdex-grpc` | `apps/interfaces/grpc/` | gRPC server |
+| `zesdex-web` | `apps/interfaces/web/` | Web frontend |
+| `zesdex-gateway` | `apps/gateway/` | CLI entry point & dispatcher |
+| `zesdex-bootstrap` | `apps/bootstrap/` | Initial data seeder |
 
-**`BREAKING CHANGE`** pada body commit → **major** (apa pun typenya).
+### Code Map
 
-Contoh:
-```
-feat(agent): add workspace-aware file search
+Detailed architecture documentation is in `docs/CODEMAPS/`:
 
-Implement context-aware search scoped to current workspace directory.
-
-BREAKING CHANGE: search results now filter by workspace scope.
-```
-
-```
-fix(ipc): handle partial frame on unix socket reconnect
-```
-
-```
-chore: update rustls to 0.23
-```
-
-### Release Workflow
-
-Push ke branch `main` akan memicu:
-1. **CI** — `cargo build --release` + `cargo test`
-2. **Semantic Release** — analisis commit → update `Cargo.toml` + `CHANGELOG.md` → git tag → GitHub Release dengan binary
+| File | Covers |
+|------|--------|
+| `docs/CODEMAPS/architecture.md` | System layout, process modes, data flow |
+| `docs/CODEMAPS/backend.md` | Provider, OAuth, IPC, workflow engine, MCP, LSP, review |
+| `docs/CODEMAPS/frontend.md` | TUI render pipeline, 16 overlays, toasts, input handling |
+| `docs/CODEMAPS/data.md` | Persistence, SQLite msglog, memory files, settings/config |
+| `docs/CODEMAPS/dependencies.md` | All Rust crates and external services |
 
 ---
 
 ## License
 
-See [LICENSE](LICENSE) for details.
+See `CHANGELOG.md` for release history.
diff --git a/apps/application/src/ports/token.rs b/apps/application/src/ports/token.rs
index c10eccc..e898610 100644
--- a/apps/application/src/ports/token.rs
+++ b/apps/application/src/ports/token.rs
@@ -23,4 +23,10 @@ pub trait TokenService: Send + Sync {
     /// Returns `Err` if the token is expired, malformed, or has an
     /// invalid signature.
     fn verify_access_token(&self, token: &str) -> Result<String>;
+
+    /// Verify a refresh token and return the embedded subject claim.
+    ///
+    /// Returns `Err` if the token is expired, malformed, or has an
+    /// invalid signature.
+    fn verify_refresh_token(&self, token: &str) -> Result<String>;
 }
diff --git a/apps/bootstrap/src/main.rs b/apps/bootstrap/src/main.rs
index 054d8e7..a23ef3d 100644
--- a/apps/bootstrap/src/main.rs
+++ b/apps/bootstrap/src/main.rs
@@ -16,7 +16,10 @@ fn main() -> anyhow::Result<()> {
     if !settings_path.exists() {
         let settings = zesdex_domain::cms::Settings::default();
         let content = serde_json::to_string_pretty(&settings)?;
-        std::fs::write(&settings_path, content)?;
+        let tmp = store.base_dir.join("settings.json.tmp");
+        std::fs::write(&tmp, &content)?;
+        std::fs::File::open(&tmp)?.sync_all()?;
+        std::fs::rename(&tmp, &settings_path)?;
         println!("  ✓ Default settings created");
     } else {
         println!("  · Settings already exist, skipping");
@@ -27,7 +30,10 @@ fn main() -> anyhow::Result<()> {
     if !config_path.exists() {
         let config = zesdex_domain::cms::AppConfig::default();
         let content = serde_json::to_string_pretty(&config)?;
-        std::fs::write(&config_path, content)?;
+        let tmp = store.base_dir.join("app_config.json.tmp");
+        std::fs::write(&tmp, &content)?;
+        std::fs::File::open(&tmp)?.sync_all()?;
+        std::fs::rename(&tmp, &config_path)?;
         println!("  ✓ Default app_config created");
     } else {
         println!("  · App config already exists, skipping");
diff --git a/apps/domain/src/cms/edit_log.rs b/apps/domain/src/cms/edit_log.rs
index d3cc5a9..7eef112 100644
--- a/apps/domain/src/cms/edit_log.rs
+++ b/apps/domain/src/cms/edit_log.rs
@@ -14,6 +14,8 @@
 //! 3. Oldest entries are evicted from the in-memory cache when
 //!    `MAX_MEMORY_ENTRIES` is exceeded (prevents unbounded growth)
 
+use std::collections::VecDeque;
+
 use serde::{Deserialize, Serialize};
 
 /// A single recorded file edit event.
@@ -47,18 +49,18 @@ pub const MAX_MEMORY_ENTRIES: usize = 10_000;
 
 /// In-memory view of a session's edit log.
 ///
-/// Wraps a `Vec<EditLogEntry>` and provides basic query helpers.
+/// Wraps a `VecDeque<EditLogEntry>` and provides basic query helpers.
 #[derive(Debug, Clone)]
 pub struct EditLog {
     /// Ordered list of edit entries (newest appended last).
-    pub entries: Vec<EditLogEntry>,
+    pub entries: VecDeque<EditLogEntry>,
 }
 
 impl EditLog {
     /// Create an empty edit log with no entries.
     pub fn new() -> Self {
         Self {
-            entries: Vec::new(),
+            entries: VecDeque::new(),
         }
     }
 
diff --git a/apps/gateway/src/main.rs b/apps/gateway/src/main.rs
index 1013b32..72efd2e 100644
--- a/apps/gateway/src/main.rs
+++ b/apps/gateway/src/main.rs
@@ -136,6 +136,7 @@ fn run_api_server(port: u16) -> anyhow::Result<()> {
     let rt = tokio::runtime::Runtime::new()?;
     rt.block_on(async {
         let store = zesdex_domain::core::Store::new();
+        store.ensure_dirs()?;
         let state = zesdex_api::ApiState::new(
             store.base_dir.clone(),
             "dev-secret",
diff --git a/apps/infrastructure/src/bgbash/control.rs b/apps/infrastructure/src/bgbash/control.rs
index e53c9bc..1384792 100644
--- a/apps/infrastructure/src/bgbash/control.rs
+++ b/apps/infrastructure/src/bgbash/control.rs
@@ -1,12 +1,20 @@
 //! Background bash control — list, cancel, and inspect background processes.
 
 use std::collections::HashMap;
-use std::sync::{Arc, Mutex};
+use std::sync::{Arc, Mutex, OnceLock};
 
 use tracing::error;
 
 use super::job::BashJob;
 
+/// Global accessor for the shared BashControl singleton.
+///
+/// Used by the Bash tool (to register jobs) and BashKill (to look them up).
+pub fn bash_control() -> &'static BashControl {
+    static BASH_CONTROL: OnceLock<BashControl> = OnceLock::new();
+    BASH_CONTROL.get_or_init(BashControl::new)
+}
+
 /// Central registry of all running background bash jobs.
 pub struct BashControl {
     jobs: Mutex<HashMap<String, Arc<BashJob>>>,
diff --git a/apps/infrastructure/src/middleware/auth.rs b/apps/infrastructure/src/middleware/auth.rs
index 491b93f..5c6f9a4 100644
--- a/apps/infrastructure/src/middleware/auth.rs
+++ b/apps/infrastructure/src/middleware/auth.rs
@@ -1,7 +1,12 @@
 //! Authentication middleware — session-lock based auth for Axum.
+//!
+//! Validates `X-Session-Id` header against the `SessionRepository` before
+//! forwarding the request to the inner service.
 
 use std::future::Future;
+use std::path::PathBuf;
 use std::pin::Pin;
+use std::sync::Arc;
 use std::task::{Context, Poll};
 
 use axum::body::Body;
@@ -9,6 +14,7 @@ use axum::http::{Request, Response, StatusCode};
 use axum::response::IntoResponse;
 use serde::{Deserialize, Serialize};
 use tower::{Layer, Service};
+use zesdex_domain::auth::{SessionId, SessionRepository};
 
 /// Identity extracted from a validated session.
 #[derive(Debug, Clone, Serialize, Deserialize)]
@@ -30,40 +36,50 @@ impl SessionIdentity {
 }
 
 /// Tower Layer that produces SessionAuthMiddleware services.
+///
+/// Holds a reference to the `SessionRepository` and the base directory
+/// needed to validate session IDs.
 #[derive(Debug, Clone)]
-pub struct SessionAuthLayer;
+pub struct SessionAuthLayer<R: SessionRepository + Send + Sync + 'static> {
+    base_dir: PathBuf,
+    repo: Arc<R>,
+}
 
-impl SessionAuthLayer {
-    pub fn new() -> Self {
-        Self
+impl<R: SessionRepository + Send + Sync + 'static> SessionAuthLayer<R> {
+    pub fn new(base_dir: PathBuf, repo: Arc<R>) -> Self {
+        Self { base_dir, repo }
     }
 }
 
-impl Default for SessionAuthLayer {
-    fn default() -> Self {
-        Self
-    }
-}
-
-impl<S> Layer<S> for SessionAuthLayer {
-    type Service = SessionAuthMiddleware<S>;
+impl<S, R> Layer<S> for SessionAuthLayer<R>
+where
+    R: SessionRepository + Send + Sync + 'static,
+{
+    type Service = SessionAuthMiddleware<S, R>;
 
     fn layer(&self, inner: S) -> Self::Service {
-        SessionAuthMiddleware { inner }
+        SessionAuthMiddleware {
+            inner,
+            base_dir: self.base_dir.clone(),
+            repo: self.repo.clone(),
+        }
     }
 }
 
 /// Tower Service that validates X-Session-Id before forwarding.
 #[derive(Debug, Clone)]
-pub struct SessionAuthMiddleware<S> {
+pub struct SessionAuthMiddleware<S, R: SessionRepository + Send + Sync + 'static> {
     inner: S,
+    base_dir: PathBuf,
+    repo: Arc<R>,
 }
 
-impl<S, ReqBody> Service<Request<ReqBody>> for SessionAuthMiddleware<S>
+impl<S, ReqBody, R> Service<Request<ReqBody>> for SessionAuthMiddleware<S, R>
 where
     S: Service<Request<ReqBody>, Response = Response<Body>> + Send + 'static,
     S::Future: Send + 'static,
     ReqBody: Send + 'static,
+    R: SessionRepository + Send + Sync + 'static,
 {
     type Response = S::Response;
     type Error = S::Error;
@@ -81,18 +97,24 @@ where
             .and_then(|v| v.to_str().ok())
             .map(|s| s.to_string());
 
-        if session_id.as_deref() != Some("valid-session") {
-            // In production, this validates against the store
-            return Box::pin(async move {
-                Ok((
-                    StatusCode::UNAUTHORIZED,
-                    "missing or invalid X-Session-Id header",
-                )
-                    .into_response())
-            });
+        // Validate the session against the repository.
+        match session_id {
+            Some(sid) => match SessionId::new(&sid) {
+                Ok(id) => match self.repo.load_session(&self.base_dir, &id) {
+                    Ok(_session) => {
+                        // Session is valid — forward the request.
+                        let fut = self.inner.call(req);
+                        return Box::pin(fut);
+                    }
+                    Err(_) => { /* fall through to 401 */ }
+                },
+                Err(_) => { /* fall through to 401 */ }
+            },
+            None => { /* fall through to 401 */ }
         }
 
-        let fut = self.inner.call(req);
-        Box::pin(fut)
+        Box::pin(async move {
+            Ok((StatusCode::UNAUTHORIZED, "missing or invalid X-Session-Id header").into_response())
+        })
     }
 }
diff --git a/apps/infrastructure/src/persistence/cms/edit_log_repo.rs b/apps/infrastructure/src/persistence/cms/edit_log_repo.rs
index c3704b8..5fbbf1e 100644
--- a/apps/infrastructure/src/persistence/cms/edit_log_repo.rs
+++ b/apps/infrastructure/src/persistence/cms/edit_log_repo.rs
@@ -1,6 +1,7 @@
 //! JSONL file–backed `EditLogRepository`.
 //! Stores `EditLog` as an append-only newline-delimited JSON file.
 
+use std::collections::VecDeque;
 use std::io::{BufRead, BufReader, Write};
 use std::path::Path;
 
@@ -18,21 +19,21 @@ impl JsonlEditLogRepository {
         Self
     }
 
-    fn load_from_disk(path: &Path) -> Vec<EditLogEntry> {
+    fn load_from_disk(path: &Path) -> VecDeque<EditLogEntry> {
         let Ok(file) = std::fs::File::open(path) else {
-            return Vec::new();
+            return VecDeque::new();
         };
         let reader = BufReader::new(file);
-        let mut entries: Vec<EditLogEntry> = Vec::new();
+        let mut entries: VecDeque<EditLogEntry> = VecDeque::new();
         for line in reader.lines() {
             let Ok(line) = line else {
                 continue;
             };
             if let Ok(entry) = serde_json::from_str::<EditLogEntry>(&line) {
                 if entries.len() >= MAX_MEMORY_ENTRIES {
-                    entries.remove(0);
+                    entries.pop_front();
                 }
-                entries.push(entry);
+                entries.push_back(entry);
             }
         }
         entries
@@ -74,14 +75,14 @@ impl EditLogRepository for JsonlEditLogRepository {
             file.write_all(line.as_bytes())?;
             file.sync_all()?;
         }
-        log.entries.push(entry);
+        log.entries.push_back(entry);
         if log.entries.len() > MAX_MEMORY_ENTRIES {
-            log.entries.remove(0);
+            log.entries.pop_front();
         }
         Ok(())
     }
 
     fn entries(&self, log: &EditLog) -> Vec<EditLogEntry> {
-        log.entries.clone()
+        log.entries.clone().into_iter().collect()
     }
 }
diff --git a/apps/infrastructure/src/persistence/cms/memory_repo.rs b/apps/infrastructure/src/persistence/cms/memory_repo.rs
index 740649a..afd0ac6 100644
--- a/apps/infrastructure/src/persistence/cms/memory_repo.rs
+++ b/apps/infrastructure/src/persistence/cms/memory_repo.rs
@@ -17,26 +17,37 @@ impl MarkdownMemoryRepository {
         Self
     }
 
+    /// Escape newlines in field values so they do not break the
+    /// line-oriented frontmatter parser.
+    fn escape_newlines(s: &str) -> String {
+        s.replace('\n', "\\n")
+    }
+
+    /// Unescape `\n` back to actual newlines after frontmatter parsing.
+    fn unescape_newlines(s: &str) -> String {
+        s.replace("\\n", "\n")
+    }
+
     fn build_frontmatter(memory: &Memory) -> String {
         let outcome_line = memory
             .outcome
             .as_ref()
-            .map(|o| format!("outcome: {o}\n"))
+            .map(|o| format!("outcome: {}\n", Self::escape_newlines(o)))
             .unwrap_or_default();
         let scope_line = memory
             .scope
             .as_ref()
-            .map(|s| format!("scope: {s}\n"))
+            .map(|s| format!("scope: {}\n", Self::escape_newlines(s)))
             .unwrap_or_default();
         let before_line = memory
             .before_snippet
             .as_ref()
-            .map(|s| format!("before: {s}\n"))
+            .map(|s| format!("before: {}\n", Self::escape_newlines(s)))
             .unwrap_or_default();
         let after_line = memory
             .after_snippet
             .as_ref()
-            .map(|s| format!("after: {s}\n"))
+            .map(|s| format!("after: {}\n", Self::escape_newlines(s)))
             .unwrap_or_default();
         let prov_line = if memory.provenances.is_empty() {
             String::new()
@@ -101,14 +112,30 @@ impl MarkdownMemoryRepository {
                 .get("updated_at")
                 .and_then(|v| v.parse().ok())
                 .unwrap_or(0),
-            outcome: front.get("outcome").cloned().filter(|s| !s.is_empty()),
+            outcome: front
+                .get("outcome")
+                .cloned()
+                .filter(|s| !s.is_empty())
+                .map(|s| Self::unescape_newlines(&s)),
             lifecycle: front
                 .get("lifecycle")
                 .cloned()
                 .unwrap_or_else(|| "new".to_string()),
-            scope: front.get("scope").cloned().filter(|s| !s.is_empty()),
-            before_snippet: front.get("before").cloned().filter(|s| !s.is_empty()),
-            after_snippet: front.get("after").cloned().filter(|s| !s.is_empty()),
+            scope: front
+                .get("scope")
+                .cloned()
+                .filter(|s| !s.is_empty())
+                .map(|s| Self::unescape_newlines(&s)),
+            before_snippet: front
+                .get("before")
+                .cloned()
+                .filter(|s| !s.is_empty())
+                .map(|s| Self::unescape_newlines(&s)),
+            after_snippet: front
+                .get("after")
+                .cloned()
+                .filter(|s| !s.is_empty())
+                .map(|s| Self::unescape_newlines(&s)),
             provenances: front
                 .get("provenances")
                 .cloned()
diff --git a/apps/infrastructure/src/persistence/iam/session_lock_repo.rs b/apps/infrastructure/src/persistence/iam/session_lock_repo.rs
index ab4d520..c1275fa 100644
--- a/apps/infrastructure/src/persistence/iam/session_lock_repo.rs
+++ b/apps/infrastructure/src/persistence/iam/session_lock_repo.rs
@@ -36,7 +36,7 @@ impl SessionLockRepository for FileSystemSessionLockRepository {
             Err(e) => return Err(RepositoryError::Io(e)),
         }
 
-        let content = std::fs::read_to_string(&path).unwrap_or_default();
+        let content = std::fs::read_to_string(&path).map_err(RepositoryError::Io)?;
         if let Ok(existing_pid) = content.trim().parse::<u32>() {
             if self.is_alive(existing_pid) {
                 return Ok(false);
@@ -46,10 +46,14 @@ impl SessionLockRepository for FileSystemSessionLockRepository {
         let tmp = path.with_extension("lock.tmp");
         {
             let mut tmp_file = std::fs::OpenOptions::new()
-                .create(true)
-                .truncate(true)
+                .create_new(true)
                 .write(true)
-                .open(&tmp)?;
+                .open(&tmp)
+                .map_err(|_| {
+                    RepositoryError::Other(
+                        "another process is replacing the lock".to_string(),
+                    )
+                })?;
             write!(tmp_file, "{pid}")?;
             tmp_file.sync_all()?;
         }
@@ -62,7 +66,7 @@ impl SessionLockRepository for FileSystemSessionLockRepository {
 
     fn unlock(&self, session_dir: &Path) -> Result<(), RepositoryError> {
         let path = session_dir.join(".lock");
-        let _ = std::fs::remove_file(path);
+        std::fs::remove_file(path)?;
         Ok(())
     }
 
diff --git a/apps/infrastructure/src/tools/bash_tools.rs b/apps/infrastructure/src/tools/bash_tools.rs
index 2f585e4..a2b4932 100644
--- a/apps/infrastructure/src/tools/bash_tools.rs
+++ b/apps/infrastructure/src/tools/bash_tools.rs
@@ -37,6 +37,11 @@ impl Tool for BashOutput {
         let job_id = arg_str(args, "job_id")?;
         info!("Getting output for job: {job_id}");
 
+        // Prevent path traversal
+        if job_id.contains('/') || job_id.contains('\\') || job_id.contains("..") {
+            anyhow::bail!("invalid job_id '{job_id}': must not contain path separators");
+        }
+
         // Read from the session's bash output directory
         let output_dir = ctx.session_dir.join("bash-outputs");
         let output_file = output_dir.join(&job_id);
@@ -80,23 +85,11 @@ impl Tool for BashKill {
     fn run(&self, _ctx: &ToolCtx, args: &Value) -> Result<String> {
         let job_id = crate::tools::arg_str(args, "job_id")?;
         info!("bash_kill called for job: {job_id}");
-        // Try to kill by PID (if job_id is numeric) or by process name
-        if let Ok(pid) = job_id.parse::<u32>() {
-            use std::process::Command;
-            match Command::new("kill").arg(pid.to_string()).output() {
-                Ok(output) if output.status.success() => {
-                    Ok(format!("Killed background job '{job_id}' (PID {pid})"))
-                }
-                Ok(output) => {
-                    let stderr = String::from_utf8_lossy(&output.stderr);
-                    Ok(format!("Failed to kill job '{job_id}': {stderr}"))
-                }
-                Err(e) => {
-                    Ok(format!("Failed to kill job '{job_id}': {e}"))
-                }
-            }
+
+        if crate::bgbash::control::bash_control().cancel(&job_id) {
+            Ok(format!("Killed background job '{job_id}'"))
         } else {
-            Ok(format!("Invalid job ID '{job_id}' — expected numeric PID"))
+            anyhow::bail!("no active background job found with ID '{job_id}'")
         }
     }
 }
diff --git a/apps/infrastructure/src/tools/fs/delete.rs b/apps/infrastructure/src/tools/fs/delete.rs
index 9a5426f..61f50df 100644
--- a/apps/infrastructure/src/tools/fs/delete.rs
+++ b/apps/infrastructure/src/tools/fs/delete.rs
@@ -45,8 +45,10 @@ impl Tool for Delete {
             fs::remove_file(&path)?;
             Ok(format!("Deleted file '{rel}'"))
         } else if path.is_dir() {
-            fs::remove_dir_all(&path)?;
-            Ok(format!("Deleted directory '{rel}' and all contents"))
+            fs::remove_dir(&path).map_err(|e| {
+                anyhow::anyhow!("failed to delete directory '{rel}': {e} (directory must be empty)")
+            })?;
+            Ok(format!("Deleted empty directory '{rel}'"))
         } else {
             anyhow::bail!("'{rel}' is neither a file nor a directory")
         }
diff --git a/apps/infrastructure/src/tools/fs/edit.rs b/apps/infrastructure/src/tools/fs/edit.rs
index 78c5e29..a3be5f1 100644
--- a/apps/infrastructure/src/tools/fs/edit.rs
+++ b/apps/infrastructure/src/tools/fs/edit.rs
@@ -56,7 +56,7 @@ impl Tool for Edit {
             anyhow::bail!("old text not found in '{}'", rel);
         }
 
-        let new_content = content.replace(&old, &new);
+        let new_content = content.replacen(&old, &new, 1);
         fs::write(&path, &new_content)?;
 
         Ok(format!(
diff --git a/apps/infrastructure/src/tools/git/git_cred.rs b/apps/infrastructure/src/tools/git/git_cred.rs
index 55920b9..380422b 100644
--- a/apps/infrastructure/src/tools/git/git_cred.rs
+++ b/apps/infrastructure/src/tools/git/git_cred.rs
@@ -3,6 +3,8 @@
 use crate::tools::{execute_cmd, Tool, ToolCtx};
 use anyhow::Result;
 use serde_json::{json, Value};
+use std::io::Write;
+use std::process::{Command, Stdio};
 
 pub struct GitCred;
 
@@ -49,10 +51,15 @@ impl Tool for GitCred {
                 let url = crate::tools::arg_str(args, "url")?;
                 let username = crate::tools::arg_str(args, "username")?;
                 let password = crate::tools::arg_str(args, "password")?;
-                let _input = format!("url={url}\nusername={username}\npassword={password}\n");
-                let _output = execute_cmd(
-                    std::process::Command::new("git").args(["credential", "approve"]),
-                )?;
+                let input = format!("url={url}\nusername={username}\npassword={password}\n");
+                let mut child = Command::new("git")
+                    .args(["credential", "approve"])
+                    .stdin(Stdio::piped())
+                    .spawn()?;
+                if let Some(ref mut stdin) = child.stdin {
+                    stdin.write_all(input.as_bytes())?;
+                }
+                child.wait()?;
                 Ok(format!("Credential stored for {url}"))
             }
             "list" => {
@@ -63,7 +70,15 @@ impl Tool for GitCred {
             }
             "erase" => {
                 let url = crate::tools::arg_str(args, "url")?;
-                let _input = format!("url={url}\n");
+                let input = format!("url={url}\n");
+                let mut child = Command::new("git")
+                    .args(["credential", "reject"])
+                    .stdin(Stdio::piped())
+                    .spawn()?;
+                if let Some(ref mut stdin) = child.stdin {
+                    stdin.write_all(input.as_bytes())?;
+                }
+                child.wait()?;
                 Ok(format!("Credential erased for {url}"))
             }
             _ => anyhow::bail!("unknown action: {}", action),
diff --git a/apps/infrastructure/src/tools/git/git_operator.rs b/apps/infrastructure/src/tools/git/git_operator.rs
index 7cbe141..f4a4c51 100644
--- a/apps/infrastructure/src/tools/git/git_operator.rs
+++ b/apps/infrastructure/src/tools/git/git_operator.rs
@@ -1,5 +1,6 @@
 //! Git operator tool — commit, push, pull, branch operations.
 
+use crate::tools::shell_filter::git::check_git_destructive;
 use crate::tools::{execute_cmd, Tool, ToolCtx};
 use anyhow::Result;
 use serde_json::{json, Value};
@@ -46,6 +47,12 @@ impl Tool for GitOperator {
             })
             .unwrap_or_default();
 
+        // Safety filter: block destructive git operations
+        let cmd_str = format!("git {} {}", operation, extra_args.join(" "));
+        if let Err(e) = check_git_destructive(&cmd_str) {
+            anyhow::bail!("blocked: {e}");
+        }
+
         let mut cmd = std::process::Command::new("git");
         cmd.arg(&operation);
         for arg in &extra_args {
diff --git a/apps/infrastructure/src/tools/shell.rs b/apps/infrastructure/src/tools/shell.rs
index 5eefb5b..1961367 100644
--- a/apps/infrastructure/src/tools/shell.rs
+++ b/apps/infrastructure/src/tools/shell.rs
@@ -61,6 +61,7 @@ impl Tool for Bash {
 
         if run_in_background {
             let job = crate::bgbash::job::spawn_bash_job(cmd);
+            crate::bgbash::control::bash_control().register(job.clone());
             return Ok(format!("Background job: {}", job.id));
         }
 
diff --git a/apps/infrastructure/src/tools/spawn.rs b/apps/infrastructure/src/tools/spawn.rs
index 0b089ad..34f4ed5 100644
--- a/apps/infrastructure/src/tools/spawn.rs
+++ b/apps/infrastructure/src/tools/spawn.rs
@@ -151,7 +151,8 @@ impl Tool for SpawnPipeline {
                     "items": {
                         "type": "object",
                         "properties": {
-                            "directive": {"type": "string", "description": "Directive for this pipeline stage"}
+                            "directive": {"type": "string", "description": "Directive for this pipeline stage"},
+                            "access": {"type": "string", "enum": ["read", "write", "full"], "description": "Access tier for this stage"}
                         },
                         "required": ["directive"]
                     },
@@ -200,17 +201,28 @@ impl Tool for SpawnPipeline {
                 .unwrap_or("")
                 .to_string();
 
+            let access_str = stage
+                .get("access")
+                .and_then(|v| v.as_str())
+                .unwrap_or("full");
+
+            let access = match access_str {
+                "read" => AccessTier::Read,
+                "write" => AccessTier::Write,
+                _ => AccessTier::Full,
+            };
+
             let subagent_ctx = SubagentContext::new(
                 directive.clone(),
                 ctx.clone(),
-                "full".to_string(),
+                access_str.to_string(),
                 base_url.clone(),
                 api_key.clone(),
                 model.clone(),
             );
 
             let result = rt.block_on(async {
-                run_agent(subagent_ctx, &directive, AccessTier::Full, ctx.clone()).await
+                run_agent(subagent_ctx, &directive, access, ctx.clone()).await
             })?;
 
             pipeline_result.push_str(&format!("Stage {}: {}\n", i, result));
diff --git a/apps/infrastructure/src/workflow/hive_mind/cycle.rs b/apps/infrastructure/src/workflow/hive_mind/cycle.rs
index e60ed74..fafec4d 100644
--- a/apps/infrastructure/src/workflow/hive_mind/cycle.rs
+++ b/apps/infrastructure/src/workflow/hive_mind/cycle.rs
@@ -1,9 +1,10 @@
 //! Hive-mind cycle execution — run one cycle of parallel nodes.
 //!
-//! Flow: load settings → resolve LLM credentials → for each directive,
-//! build a SubagentContext and call run_agent → collect NodeOutputs.
+//! Flow: load settings → resolve LLM credentials → run all directives in the
+//! cycle concurrently via try_join_all → collect Vec<NodeOutput>.
 
 use anyhow::Result;
+use futures_util::future::try_join_all;
 use tracing::info;
 
 use zesdex_domain::cms::{AppConfigRepository, SettingsRepository};
@@ -21,8 +22,9 @@ use crate::workflow::hive_mind::types::{CognitiveCycle, NodeOutput};
 /// Flow:
 ///   1. Load `Settings` and `AppConfig` from the store directory.
 ///   2. Resolve provider, model, base_url, and api_key.
-///   3. For each directive → build `SubagentContext` → `run_agent` (Full access).
-///   4. Collect `NodeOutput` results.
+///   3. Spawn all directives concurrently — each builds a `SubagentContext`
+///      and calls `run_agent` (Full access).
+///   4. `try_join_all` waits for all to complete, then collect `NodeOutput`s.
 pub async fn execute_cycle(
     cycle: &CognitiveCycle,
     tool_ctx: &ToolCtx,
@@ -52,25 +54,37 @@ pub async fn execute_cycle(
 
     let api_key = crate::llm::provider::resolve_api_key(&settings, &app_config);
 
-    let mut outputs = Vec::new();
-    for (i, directive) in cycle.directives.iter().enumerate() {
-        let ctx = SubagentContext::new(
-            directive.clone(),
-            tool_ctx.clone(),
-            "full".to_string(),
-            base_url.clone(),
-            api_key.clone(),
-            model.clone(),
-        );
+    let cycle_index = cycle.index;
 
-        let result = run_agent(ctx, directive, AccessTier::Full, tool_ctx.clone()).await?;
+    // Run all directives in this cycle concurrently.
+    let handles: Vec<_> = cycle
+        .directives
+        .iter()
+        .enumerate()
+        .map(|(i, directive)| {
+            let dir = directive.clone();
+            let ctx = SubagentContext::new(
+                dir.clone(),
+                tool_ctx.clone(),
+                "full".to_string(),
+                base_url.clone(),
+                api_key.clone(),
+                model.clone(),
+            );
+            let tc = tool_ctx.clone();
 
-        outputs.push(NodeOutput {
-            id: format!("Node-{}-{}", cycle.index, i),
-            directive: directive.clone(),
-            output: result,
-        });
-    }
+            async move {
+                let result = run_agent(ctx, &dir, AccessTier::Full, tc).await?;
+                Ok::<NodeOutput, anyhow::Error>(NodeOutput {
+                    id: format!("Node-{}-{}", cycle_index, i),
+                    directive: dir,
+                    output: result,
+                })
+            }
+        })
+        .collect();
 
-    Ok(outputs)
+    let results = try_join_all(handles).await?;
+
+    Ok(results)
 }
diff --git a/apps/interfaces/api/src/handlers/auth.rs b/apps/interfaces/api/src/handlers/auth.rs
index 9e8de00..bac6057 100644
--- a/apps/interfaces/api/src/handlers/auth.rs
+++ b/apps/interfaces/api/src/handlers/auth.rs
@@ -203,7 +203,7 @@ pub async fn refresh_handler(
     // Verify the refresh token and extract the subject
     let sub = state
         .token_service
-        .verify_access_token(&req.refresh_token)
+        .verify_refresh_token(&req.refresh_token)
         .map_err(|_| ApiError::Unauthorized("Invalid or expired refresh token".into()))?;
 
     // Generate a fresh token pair
diff --git a/apps/interfaces/api/src/handlers/chat.rs b/apps/interfaces/api/src/handlers/chat.rs
index 7917092..84746de 100644
--- a/apps/interfaces/api/src/handlers/chat.rs
+++ b/apps/interfaces/api/src/handlers/chat.rs
@@ -109,18 +109,21 @@ pub async fn chat_completions_handler(
 
     // Call the LLM provider (non-streaming)
     //
-    // We create a temporary LlmClient with the overridden model so we
-    // don't mutate the shared state's client.
+    // When the requested model matches the shared client we reuse it to
+    // avoid allocating a new HTTP connection.  Otherwise we create a
+    // temporary LlmClient with the requested model — the ownership
+    // lives on the stack via `temp_client`.
+    #[allow(unused_assignments)]
+    let mut temp_client: Option<zesdex_infrastructure::llm::LlmClient> = None;
     let llm_client = if model == state.llm_client.model {
-        // Use the shared client directly
         &state.llm_client
     } else {
-        // Create a modified client for this request (only borrows, but
-        // we need to own it for the call — handled below)
-        //
-        // For simplicity, use the shared client with its model. A full
-        // implementation would override the model per request.
-        &state.llm_client
+        temp_client = Some(zesdex_infrastructure::llm::LlmClient::new(
+            state.llm_client.api_key.clone(),
+            model,
+            Some(state.llm_client.base_url.clone()),
+        ));
+        temp_client.as_ref().unwrap()
     };
 
     let (response, usage) = llm_client
diff --git a/apps/interfaces/api/src/handlers/conversations.rs b/apps/interfaces/api/src/handlers/conversations.rs
index 02c221e..9808b83 100644
--- a/apps/interfaces/api/src/handlers/conversations.rs
+++ b/apps/interfaces/api/src/handlers/conversations.rs
@@ -103,29 +103,44 @@ pub async fn add_message_handler(
     ))
 }
 
-/// DELETE /sessions/:id/conversations/:cid — delete a message from a conversation.
+/// DELETE /sessions/:id/conversations/:cid — delete a single message by index.
 ///
-/// Note: the `cid` parameter currently identifies the message index or the
-/// entire conversation. For simplicity, this deletes the entire conversation
-/// and creates a fresh one. A more sophisticated implementation would remove
-/// a single message by index.
+/// ## Flow
+///
+/// 1. Extract session ID and message index from the path.
+/// 2. Load the conversation.
+/// 3. Remove the message at `cid` (zero-based index).
+/// 4. Persist the updated conversation.
 ///
 /// ## Errors
 ///
-/// - `404 Not Found` — conversation not found.
+/// - `400 Bad Request` — session ID is empty or `cid` is not a valid integer.
+/// - `404 Not Found` — conversation or message index not found.
 #[tracing::instrument(skip(state))]
 pub async fn delete_message_handler(
     State(state): State<Arc<ApiState>>,
-    Path((id, _cid)): Path<(String, String)>,
+    Path((id, cid)): Path<(String, String)>,
 ) -> Result<axum::http::StatusCode, ApiError> {
     if id.is_empty() {
         return Err(ApiError::BadRequest("Session ID is required".into()));
     }
 
-    // Load conversation and clear all messages
+    // Parse the message index from the path
+    let index: usize = cid
+        .parse()
+        .map_err(|_| ApiError::BadRequest(format!("Invalid message index: {cid}")))?;
+
+    // Load conversation and remove the specific message by index
     let mut conversation = state.conversation_service.load_conversation(&id)?;
 
-    conversation.messages.clear();
+    if index >= conversation.messages.len() {
+        return Err(ApiError::NotFound(format!(
+            "Message index {index} out of bounds (max: {})",
+            conversation.messages.len().saturating_sub(1)
+        )));
+    }
+
+    conversation.messages.remove(index);
     state
         .conversation_service
         .save_conversation(&conversation)?;
diff --git a/apps/interfaces/api/src/lib.rs b/apps/interfaces/api/src/lib.rs
index a022d2d..f95107e 100644
--- a/apps/interfaces/api/src/lib.rs
+++ b/apps/interfaces/api/src/lib.rs
@@ -56,10 +56,17 @@ pub fn build_router(state: ApiState) -> Router {
     // CORS layer — permissive for local daemon / development use
     let cors = CorsLayer::permissive();
 
+    // JWT auth middleware — validates Bearer tokens on all API routes.
+    // Health and auth endpoints (login/register/refresh) are also
+    // protected; adjust route ordering or add an allow-list inside the
+    // middleware if public access is needed.
+    let jwt_auth = middleware::auth::JwtAuthLayer::new(shared_state.clone());
+
     // Combine all sub-routers under a versioned prefix
     Router::new()
         .nest("/api/v1", api_v1_router())
         .layer(cors)
+        .layer(jwt_auth)
         .with_state(shared_state)
 }
 
diff --git a/apps/interfaces/api/src/state.rs b/apps/interfaces/api/src/state.rs
index 9bd2259..5086071 100644
--- a/apps/interfaces/api/src/state.rs
+++ b/apps/interfaces/api/src/state.rs
@@ -120,6 +120,19 @@ impl TokenService for JwtTokenService {
         let claims = verify_token(&self.secret, token)?;
         Ok(claims.sub)
     }
+
+    /// Verify a refresh token and return the subject claim.
+    ///
+    /// Delegates to the same JWT verification function as access tokens;
+    /// the signature algorithm and secret are shared. Expiry validation
+    /// is handled by the JWT library against the `exp` claim embedded
+    /// in the token payload.
+    fn verify_refresh_token(&self, token: &str) -> anyhow::Result<String> {
+        use zesdex_infrastructure::auth::jwt::verify_token;
+
+        let claims = verify_token(&self.secret, token)?;
+        Ok(claims.sub)
+    }
 }
 
 // ---------------------------------------------------------------------------
diff --git a/apps/interfaces/daemon/src/handler.rs b/apps/interfaces/daemon/src/handler.rs
index 74b7490..a0670f7 100644
--- a/apps/interfaces/daemon/src/handler.rs
+++ b/apps/interfaces/daemon/src/handler.rs
@@ -230,8 +230,8 @@ fn handle_tick(state: &mut AppStateRest) {
             }
             TurnEvent::Usage { tokens_in, tokens_out } => {
                 if let Some(ref mut rt) = state.session_runtime {
-                    rt.usage.tokens_in += tokens_in;
-                    rt.usage.tokens_out += tokens_out;
+                    rt.usage.tokens_in = rt.usage.tokens_in.saturating_add(tokens_in);
+                    rt.usage.tokens_out = rt.usage.tokens_out.saturating_add(tokens_out);
                 }
             }
             TurnEvent::ReviewUsage {
@@ -239,8 +239,8 @@ fn handle_tick(state: &mut AppStateRest) {
                 tokens_out,
             } => {
                 if let Some(ref mut rt) = state.session_runtime {
-                    rt.usage.tokens_in += tokens_in;
-                    rt.usage.tokens_out += tokens_out;
+                    rt.usage.tokens_in = rt.usage.tokens_in.saturating_add(tokens_in);
+                    rt.usage.tokens_out = rt.usage.tokens_out.saturating_add(tokens_out);
                 }
             }
             TurnEvent::Done => {
@@ -524,11 +524,8 @@ pub fn handle_key(key: KeyEvent, state: &mut AppStateRest) -> Vec<Action> {
     // ── Normal mode ───────────────────────────────────────────────────────
     match key.code {
         KeyCode::Char('c') if key.modifiers.contains(KeyModifiers::CONTROL) => {
-            if state.misc.overlay.is_active() {
-                vec![Action::QuitConfirm]
-            } else {
-                vec![Action::ForceQuit]
-            }
+            // Always show quit-confirm, regardless of overlay state.
+            vec![Action::QuitConfirm]
         }
         KeyCode::Char('d') if key.modifiers.contains(KeyModifiers::CONTROL) => {
             vec![Action::CloseOverlay]
@@ -552,7 +549,14 @@ pub fn handle_key(key: KeyEvent, state: &mut AppStateRest) -> Vec<Action> {
         }
         KeyCode::Enter => {
             if state.misc.overlay.is_active() {
-                vec![Action::CloseOverlay]
+                match state.misc.overlay {
+                    Overlay::QuitConfirm => vec![Action::ForceQuit],
+                    Overlay::ClearConfirm => vec![Action::SystemNote {
+                        kind: "clear".to_string(),
+                        message: "cleared".to_string(),
+                    }],
+                    _ => vec![Action::CloseOverlay],
+                }
             } else if state.input.autocomplete_visible {
                 // Select the current autocomplete candidate
                 if !state.input.autocomplete_candidates.is_empty() {
diff --git a/apps/interfaces/tui/src/action.rs b/apps/interfaces/tui/src/action.rs
index 5225110..d4875e5 100644
--- a/apps/interfaces/tui/src/action.rs
+++ b/apps/interfaces/tui/src/action.rs
@@ -151,6 +151,11 @@ pub fn apply_action(state: &mut crate::state::AppStateRest, action: Action) {
                     zesdex_infrastructure::TurnEvent::Error(msg) => {
                         state.toast_error(msg);
                     }
+                    zesdex_infrastructure::TurnEvent::Compacted(msgs) => {
+                        if let Some(ref mut rt) = state.session_runtime {
+                            rt.messages = msgs;
+                        }
+                    }
                     zesdex_infrastructure::TurnEvent::Done => {
                         if let Ok(mut flag) = state.turn_in_flight_flag.lock() {
                             *flag = false;
diff --git a/apps/interfaces/tui/src/turn.rs b/apps/interfaces/tui/src/turn.rs
index b65e142..c28d829 100644
--- a/apps/interfaces/tui/src/turn.rs
+++ b/apps/interfaces/tui/src/turn.rs
@@ -173,6 +173,11 @@ fn run_turn(
         }
     }
 
+    // Propagate accumulated messages back to session_runtime so the next
+    // turn starts with the full history (assistant replies + tool results).
+    // TurnEvent::Compacted already exists on the enum and is handled in
+    // action.rs to write back to state.session_runtime.messages.
+    push_event(turn_events, TurnEvent::Compacted(messages.clone()));
     push_event(turn_events, TurnEvent::Done);
     mark_done(in_flight);
 }