refactor: rombak arsitektur file ke modular clean-arch (vertikal per-feature)

Organisasi ulang layer-first (domain/application/infrastructure) menjadi
vertikal per-feature, behavior tidak berubah:

- src/shared/domain/  -> fondasi bersama (ex-domain/core): message, provider,
  tool_call, tool_result, store, error, usage, conversation
- src/features/agent/ -> LLM turn loop: domain (TurnEvent, AgentTurnParams) +
  application (turn_service, ports) + infrastructure (llm LlmClient + tools)
- src/features/cms/   -> settings/conversation/memory persistence: domain +
  application (services) + infrastructure (persistence repos)
- src/features/subagent/ -> orchestration: domain (AccessTier) + infrastructure
  (engine runner, context, provider, delegate, spawn_tools)
- src/features/workflow/ -> multi-phase + hive-mind: domain + infrastructure
- src/interfaces/     -> cli + tui (outer ring) tetap

Subagent-runner (engine.ts runAgent, division.ts toolsFor) dipindah ke
features/subagent (bukan agent tools) utk memutus coupling agent<->subagent.

Alias tsconfig: @zesdex/domain -> shared/domain, + @zesdex/agent,
@zesdex/agent-infra, @zesdex/cms, @zesdex/subagent, @zesdex/workflow, @zesdex/shared.
Bersihkan dead: application/ports PasswordService/TokenService/AuthService.
compose.ts (composition root) & bootstrap repoint ke barrel feature.

Gates: tsc --noEmit 0 error, bun test 70 pass/0 fail, bun build 147 modules,
./dist/zesdex --headless -> real turn OK.

src/application/index.ts

@@ -1,8 +0,0 @@
-/**
- * Zesdex Application Layer — port traits, use cases, turn service.
- * Depends only on @zesdex/domain. Higher-level ports implemented by
- * infrastructure adapters.
- */
-export * from "./ports/index.ts";
-export * from "./agent/index.ts";
-export * from "./cms/index.ts";

src/domain/cms/conversation.ts

@@ -1,7 +0,0 @@
-/**
- * Re-export of conversation types from core (matches Rust `cms/conversation.rs`).
- */
-export type { Conversation } from "../core/conversation.ts";
-export type { ChatMessage, Role } from "../core/message.ts";
-export { newConversation, pushMessage, rebuildSystem, toApiMessages } from "../core/conversation.ts";
-export { Roles } from "../core/message.ts";

src/domain/index.ts

@@ -1,9 +0,0 @@
-/**
- * Zesdex Domain Layer — pure types, value objects, and port interfaces.
- * Zero framework dependencies, zero I/O. Mirrors the Rust `zesdex-domain` crate.
- */
-export * from "./core/index.ts";
-export * from "./cms/index.ts";
-export * from "./agent/index.ts";
-export * from "./subagent/mod.ts";
-export * from "./workflow/mod.ts";

src/features/agent/application/index.ts

@@ -14,7 +14,7 @@ export interface ToolExecutor {
 
 /** Service for running agent turns asynchronously. */
 export interface AgentTurnService {
-  runTurn(params: import("@zesdex/domain").AgentTurnParams): Promise<void>;
+  runTurn(params: import("@zesdex/agent").AgentTurnParams): Promise<void>;
 }
 
 export * from "./turn_service.ts";

src/features/agent/application/ports.ts

@@ -1,6 +1,7 @@
 /**
- * Port traits (interfaces) to external services. Mirrors `apps/application/src/ports/`.
- * Concrete implementations live in the infrastructure layer.
+ * Port traits (interfaces) that the Agent application layer exposes to
+ * its infrastructure. Concrete implementations live in
+ * `features/agent/infrastructure/`.
  */
 import type { ChatMessage, StreamEvent, ToolDef } from "@zesdex/domain";
 
@@ -31,23 +32,3 @@ export interface ProviderService {
     signal?: AbortSignal,
   ): Promise<{ message: ChatMessage; usage: [number, number] | null }>;
 }
-
-/** Abstraction for password hashing and verification. */
-export interface PasswordService {
-  hash(password: string): Promise<string>;
-  verify(password: string, hash: string): Promise<boolean>;
-}
-
-/** Abstraction for JWT-based token generation and verification. */
-export interface TokenService {
-  /** Generate an `[access, refresh]` token pair for the given subject. */
-  generateTokens(sub: string): [string, string];
-  verifyAccessToken(token: string): string;
-  verifyRefreshToken(token: string): string;
-}
-
-/** High-level authentication service combining password + token issuance. */
-export interface AuthService {
-  authenticate(password: string, hash: string): Promise<boolean>;
-  issueTokens(sub: string): [string, string];
-}

src/features/agent/application/turn_service.ts

@@ -3,23 +3,25 @@
  * `apps/application/src/agent/turn_service.rs`.
  */
 import {
-  type AgentTurnParams,
   type ChatMessage,
   type StreamEvent,
   type ToolCall,
   type ToolDef,
-  type TurnEventSink,
   type JsonValue,
   systemMessage,
   userMessage,
   assistantMessage,
   toolResultMessage,
+  sanitizeToolArguments,
+} from "@zesdex/domain";
+import {
+  type AgentTurnParams,
+  type TurnEventSink,
   mainAgentPromptWithProjectContext,
   compactionPrompt,
   errorRecoveryNote,
-  sanitizeToolArguments,
-} from "@zesdex/domain";
-import type { ProviderService } from "../ports/index.ts";
+} from "@zesdex/agent";
+import type { ProviderService } from "./ports.ts";
 import type { ToolExecutor } from "./index.ts";
 
 /* -------------------------------------------------------------------------- */

src/features/agent/domain/mod.ts

@@ -2,7 +2,7 @@
  * Domain types for agent lifecycle: turn events, session runtime, progress.
  * Mirrors `apps/domain/src/agent/mod.rs`.
  */
-import type { ChatMessage, JsonValue, ToolCallResult, UsageStats } from "../core/index.ts";
+import type { ChatMessage, JsonValue, ToolCallResult, UsageStats } from "@zesdex/domain";
 import type { AgentProgress } from "./progress.ts";
 
 /** Which kind of caller (main agent vs subagent vs reviewer) is invoking a tool. */

src/features/agent/index.ts

@@ -0,0 +1,5 @@
+/** Agent feature — LLM turn loop, tool-execution runtime, subagent-spawning tools.
+ *  Vertical slice: domain (turn events/runtime) → application (turn service + ports)
+ *  → infrastructure (LLM client + tool registry/executor). */
+export * from "./domain/index.ts";
+export * from "./application/index.ts";

src/features/agent/infrastructure/index.ts

@@ -0,0 +1,6 @@
+/** Agent infrastructure — concrete LLM client + tool-execution runtime.
+ *  Consumed by the composition root. */
+export { LlmClient, resolveApiKey } from "./llm/provider.ts";
+export { InfrastructureToolExecutor } from "./tools/executor.ts";
+export { allTools, toolDefs } from "./tools/registry.ts";
+export { type ToolCtx } from "./tools/context.ts";

src/features/agent/infrastructure/llm/provider.ts

@@ -8,14 +8,12 @@ import {
   type StreamEvent,
   type ToolCall,
   type ToolDef,
-  type Settings,
-  type AppConfig,
   SseParser,
   Roles,
-  DEFAULT_API_BASE,
-  DEFAULT_MODEL,
 } from "@zesdex/domain";
-import type { ProviderService } from "@zesdex/application";
+import type { Settings, AppConfig } from "@zesdex/cms";
+import { DEFAULT_API_BASE, DEFAULT_MODEL } from "@zesdex/agent";
+import type { ProviderService } from "../../application/ports.ts";
 
 const DEFAULT_BASE_URL = DEFAULT_API_BASE;
 const REQUEST_TIMEOUT_MS = 600_000;

src/features/agent/infrastructure/tools/bash_tools.ts

@@ -7,7 +7,7 @@ import * as path from "node:path";
 import type { JsonValue } from "@zesdex/domain";
 import { type Tool, type ToolCtx } from "./mod.ts";
 import { argStr } from "./util.ts";
-import { bashControl } from "../bgbash/control.ts";
+import { bashControl } from "./bgbash/control.ts";
 
 /** Get the output of a background bash job by ID. */
 export class BashOutput implements Tool {

src/features/agent/infrastructure/tools/best_practice/tools.ts

@@ -2,8 +2,8 @@
  * Built-in best-practice tools. Mirrors `tools/best_practice.rs`.
  */
 import type { JsonValue } from "@zesdex/domain";
-import { type Tool, type ToolCtx } from "../tools/mod.ts";
-import { argStr, optStr } from "../tools/util.ts";
+import { type Tool, type ToolCtx } from "../mod.ts";
+import { argStr, optStr } from "../util.ts";
 import { BestPracticeEngine } from "./engine.ts";
 
 const engine = new BestPracticeEngine();

src/features/agent/infrastructure/tools/context.ts

@@ -2,7 +2,7 @@
  * Tool execution context — shared state passed to every `Tool.run` call.
  * Mirrors `apps/infrastructure/src/tools/context.rs`.
  */
-import type { Origin, TurnEvent } from "@zesdex/domain";
+import type { Origin, TurnEvent } from "@zesdex/agent";
 
 /** Graduated check rule from project config. */
 export interface GraduatedCheck {

src/features/agent/infrastructure/tools/event_sink.ts

@@ -2,7 +2,7 @@
  * Simple sink adapter that wraps a TurnEvent[] (array-based) into the
  * TurnEventSink interface, providing a `push` method and a no-op `drain`.
  */
-import type { TurnEvent, TurnEventSink } from "@zesdex/domain";
+import type { TurnEvent, TurnEventSink } from "@zesdex/agent";
 
 /**
  * Create a TurnEventSink backed by a plain array.

src/features/agent/infrastructure/tools/memory/forget.ts

@@ -2,7 +2,7 @@
  * Delete a memory by name. Mirrors `tools/memory/forget.rs`.
  */
 import type { JsonValue } from "@zesdex/domain";
-import { MarkdownMemoryRepository } from "../../persistence/cms/memory_repo.ts";
+import { MarkdownMemoryRepository } from "@zesdex/cms";
 import { type Tool, type ToolCtx } from "../mod.ts";
 import { argStr } from "../util.ts";
 import { resolveMemoryDir } from "./mod.ts";

src/features/agent/infrastructure/tools/memory/recall.ts

@@ -2,7 +2,7 @@
  * Recall previously saved memories. Mirrors `tools/memory/recall.rs`.
  */
 import type { JsonValue } from "@zesdex/domain";
-import { MarkdownMemoryRepository } from "../../persistence/cms/memory_repo.ts";
+import { MarkdownMemoryRepository } from "@zesdex/cms";
 import { type Tool, type ToolCtx } from "../mod.ts";
 import { optStr } from "../util.ts";
 import { resolveMemoryDir } from "./mod.ts";

src/features/agent/infrastructure/tools/memory/remember.ts

@@ -2,7 +2,7 @@
  * Remember a lesson or fact as persistent memory. Mirrors `tools/memory/remember.rs`.
  */
 import type { JsonValue } from "@zesdex/domain";
-import { MarkdownMemoryRepository } from "../../persistence/cms/memory_repo.ts";
+import { MarkdownMemoryRepository } from "@zesdex/cms";
 import { type Tool, type ToolCtx } from "../mod.ts";
 import { argStr, optStr } from "../util.ts";
 import { resolveMemoryDir } from "./mod.ts";

src/features/agent/infrastructure/tools/parallel_delegate.ts

@@ -59,7 +59,7 @@ export class ParallelDelegate implements Tool {
 
     // Delegate to subagent engine if available, else report the breakdown.
     try {
-      const { runParallelDelegation } = await import("../subagent/delegate.ts");
+      const { runParallelDelegation } = await import("../../../subagent/infrastructure/delegate.ts");
       return await runParallelDelegation(task, directives, synthesize, ctx);
     } catch (e) {
       const msg = (e as Error).message;

src/features/agent/infrastructure/tools/plan.ts

@@ -1,7 +1,8 @@
 /** Plan management tools — enter and mark ready. Mirrors `tools/plan.rs`. */
 import * as fs from "node:fs";
 import * as path from "node:path";
-import type { JsonValue, TurnEvent } from "@zesdex/domain";
+import type { JsonValue } from "@zesdex/domain";
+import type { TurnEvent } from "@zesdex/agent";
 import { type Tool, type ToolCtx } from "./mod.ts";
 import { argStr } from "./util.ts";
 

src/features/agent/infrastructure/tools/registry.ts

@@ -25,7 +25,7 @@ import { Cd, DirList, DirCacheUpdate, Pong, Todowrite, Todofinish } from "./util
 import { WebSearch } from "./web_search.ts";
 import { SemanticSearch, RebuildIndex, ListSymbols } from "./semantic/index.ts";
 import { ParallelDelegate } from "./parallel_delegate.ts";
-import { BestPractice, CommitConvention } from "../best_practice/tools.ts";
+import { BestPractice, CommitConvention } from "./best_practice/tools.ts";
 
 /** Construct one instance of every built-in tool. */
 export function allTools(): Tool[] {

src/features/agent/infrastructure/tools/shell/bash.ts

@@ -39,8 +39,8 @@ export class Bash implements Tool {
 
     if (runInBackground) {
       // Background jobs handled via bgbash registry
-      const { spawnBashJob } = await import("../../bgbash/job.ts");
-      const { bashControl } = await import("../../bgbash/control.ts");
+      const { spawnBashJob } = await import("../bgbash/job.ts");
+      const { bashControl } = await import("../bgbash/control.ts");
       const job = spawnBashJob(cmd);
       bashControl().register(job);
       return `Background job: ${job.id}`;

src/features/agent/infrastructure/tools/spawn.ts

@@ -33,7 +33,7 @@ export class SpawnAgents implements Tool {
   async run(ctx: ToolCtx, args: JsonValue): Promise<string> {
     const agents = reqArray(args, "agents");
     try {
-      const { spawnAgents } = await import("../subagent/spawn_tools.ts");
+      const { spawnAgents } = await import("../../../subagent/infrastructure/spawn_tools.ts");
       return await spawnAgents(agents as Array<{ directive: string; access: string }>, ctx);
     } catch (e) {
       const msg = (e as Error).message;
@@ -71,7 +71,7 @@ export class SpawnPipeline implements Tool {
   async run(ctx: ToolCtx, args: JsonValue): Promise<string> {
     const stages = reqArray(args, "stages");
     try {
-      const { spawnPipeline } = await import("../subagent/spawn_tools.ts");
+      const { spawnPipeline } = await import("../../../subagent/infrastructure/spawn_tools.ts");
       return await spawnPipeline(stages as Array<{ directive: string; access: string }>, ctx);
     } catch (e) {
       const msg = (e as Error).message;