fix(instance): restore InstanceBootstrap init parameter for non-Effect entry points

The v1.14.32 refactoring converted LoadInput.init from a Promise callback
to an Effect, and InstanceBootstrap from a bare Effect to a Service. The
httpapi middleware was updated correctly, but the legacy Hono middleware
and CLI entry points simply deleted the init parameter instead of
adapting it, causing InstanceBootstrap (including plugin initialization
-> config hook -> agent registration) to never execute for these paths.

Changes:
- Add InstanceBootstrap.defaultLayer to AppRuntime's AppLayer so the
  bootstrap run Effect shares the same service instances as AppRuntime
- Add getBootstrapRunEffect() helper that lazily resolves the run Effect
  from AppRuntime (cached after first call)
- Restore init parameter in InstanceMiddleware, workspace router, CLI
  bootstrap, TUI worker, and project reload
- Add plugin.init() defense-in-depth inside Agent state builder to
  protect CLI commands and other init-less entry points

Author: HyeokjaeLee

packages/opencode/src/agent/agent.ts

@@ -80,6 +80,7 @@ export const layer = Layer.effect(
     const state = yield* InstanceState.make<State>(
       Effect.fn("Agent.state")(function* (ctx) {
         const cfg = yield* config.get()
+        yield* plugin.init()
         const skillDirs = yield* skill.dirs()
         const whitelistedDirs = [
           Truncate.GLOB,

packages/opencode/src/cli/bootstrap.ts

@@ -1,9 +1,11 @@
 import { Instance } from "../project/instance"
 import { InstanceStore } from "../project/instance-store"
+import { getBootstrapRunEffect } from "../effect/app-runtime"
 
 export async function bootstrap<T>(directory: string, cb: () => Promise<T>) {
   return Instance.provide({
     directory,
+    init: await getBootstrapRunEffect(),
     fn: async () => {
       try {
         const result = await cb()

packages/opencode/src/cli/cmd/tui/worker.ts

@@ -10,7 +10,7 @@ import { GlobalBus } from "@/bus/global"
 import { Flag } from "@opencode-ai/core/flag/flag"
 import { writeHeapSnapshot } from "node:v8"
 import { Heap } from "@/cli/heap"
-import { AppRuntime } from "@/effect/app-runtime"
+import { AppRuntime, getBootstrapRunEffect } from "@/effect/app-runtime"
 import { ensureProcessMetadata } from "@opencode-ai/core/util/opencode-process"
 
 ensureProcessMetadata("worker")
@@ -77,6 +77,7 @@ export const rpc = {
   async checkUpgrade(input: { directory: string }) {
     await Instance.provide({
       directory: input.directory,
+      init: await getBootstrapRunEffect(),
       fn: async () => {
         await upgrade().catch(() => {})
       },

packages/opencode/src/effect/app-runtime.ts

@@ -1,4 +1,4 @@
-import { Layer, ManagedRuntime } from "effect"
+import { Effect, Layer, ManagedRuntime } from "effect"
 import { attach } from "./run-service"
 import * as Observability from "@opencode-ai/core/effect/observability"
 
@@ -39,6 +39,7 @@ import { Command } from "@/command"
 import { Truncate } from "@/tool/truncate"
 import { ToolRegistry } from "@/tool/registry"
 import { Format } from "@/format"
+import { InstanceBootstrap } from "@/project/bootstrap"
 import { InstanceStore } from "@/project/instance-store"
 import { Project } from "@/project/project"
 import { Vcs } from "@/project/vcs"
@@ -91,6 +92,7 @@ export const AppLayer = Layer.mergeAll(
   Truncate.defaultLayer,
   ToolRegistry.defaultLayer,
   Format.defaultLayer,
+  InstanceBootstrap.defaultLayer,
   InstanceStore.defaultLayer,
   Project.defaultLayer,
   Vcs.defaultLayer,
@@ -128,3 +130,15 @@ export const AppRuntime: Runtime = {
   },
   dispose: () => rt.dispose(),
 }
+
+let bootstrapRun: Promise<Effect.Effect<void>>
+export function getBootstrapRunEffect(): Promise<Effect.Effect<void>> {
+  if (!bootstrapRun) {
+    bootstrapRun = AppRuntime.runPromise(
+      Effect.gen(function* () {
+        return (yield* InstanceBootstrap.Service).run
+      }),
+    )
+  }
+  return bootstrapRun
+}

packages/opencode/src/server/routes/instance/middleware.ts

@@ -1,6 +1,6 @@
 import type { MiddlewareHandler } from "hono"
 import { Instance } from "@/project/instance"
-import { AppRuntime } from "@/effect/app-runtime"
+import { getBootstrapRunEffect } from "@/effect/app-runtime"
 import { AppFileSystem } from "@opencode-ai/core/filesystem"
 import { WorkspaceContext } from "@/control-plane/workspace-context"
 import { WorkspaceID } from "@/control-plane/schema"
@@ -23,6 +23,7 @@ export function InstanceMiddleware(workspaceID?: WorkspaceID): MiddlewareHandler
       async fn() {
         return Instance.provide({
           directory,
+          init: await getBootstrapRunEffect(),
           async fn() {
             return next()
           },

packages/opencode/src/server/routes/instance/project.ts

@@ -8,7 +8,7 @@ import z from "zod"
 import { ProjectID } from "@/project/schema"
 import { errors } from "../../error"
 import { lazy } from "@/util/lazy"
-import { AppRuntime } from "@/effect/app-runtime"
+import { getBootstrapRunEffect } from "@/effect/app-runtime"
 import { jsonRequest, runRequest } from "./trace"
 
 export const ProjectRoutes = lazy(() =>
@@ -82,7 +82,7 @@ export const ProjectRoutes = lazy(() =>
           Project.Service.use((svc) => svc.initGit({ directory: dir, project: prev })),
         )
         if (next.id === prev.id && next.vcs === prev.vcs && next.worktree === prev.worktree) return c.json(next)
-        await InstanceStore.reloadInstance({ directory: dir, worktree: dir, project: next })
+        await InstanceStore.reloadInstance({ directory: dir, worktree: dir, project: next, init: await getBootstrapRunEffect() })
         return c.json(next)
       },
     )

packages/opencode/src/server/workspace.ts

@@ -5,10 +5,10 @@ import { WorkspaceID } from "@/control-plane/schema"
 import { WorkspaceContext } from "@/control-plane/workspace-context"
 import { Workspace } from "@/control-plane/workspace"
 import { Flag } from "@opencode-ai/core/flag/flag"
+import { getBootstrapRunEffect, AppRuntime } from "@/effect/app-runtime"
 import { Instance } from "@/project/instance"
 import { Session } from "@/session/session"
 import { SessionID } from "@/session/schema"
-import { AppRuntime } from "@/effect/app-runtime"
 import { Effect } from "effect"
 import * as Log from "@opencode-ai/core/util/log"
 import { ServerProxy } from "./proxy"
@@ -94,11 +94,13 @@ export function WorkspaceRouterMiddleware(upgrade: UpgradeWebSocket): Middleware
     const target = await adapter.target(workspace)
 
     if (target.type === "local") {
+      const init = await getBootstrapRunEffect()
       return WorkspaceContext.provide({
         workspaceID: WorkspaceID.make(workspaceID),
         fn: () =>
           Instance.provide({
             directory: target.directory,
+            init,
             async fn() {
               return next()
             },