fix(core): restore external directory defaults

packages/core/src/config/plugin/agent.ts

@@ -12,6 +12,7 @@ import { ConfigAgentV1 } from "../../v1/config/agent"
 import { ConfigMigrateV1 } from "../../v1/config/migrate"
 import { Global } from "../../global"
 import { PermissionV2 } from "../../permission"
+import { SHELL_OUTPUT_GLOB } from "../../permission/defaults"
 import type { LocationMutation } from "../../location-mutation"
 import type { ReadTool } from "../../tool/read"
 import type { EditTool } from "../../tool/edit"
@@ -112,6 +113,23 @@ export const Plugin = define({
           })
         }
       }
+
+      // Internal shell output remains readable through broad external-directory denials.
+      // An exact deny still lets users explicitly revoke access to these files.
+      for (const current of draft.list()) {
+        draft.update(current.id, (agent) => {
+          const denied = agent.permissions.some(
+            (rule) =>
+              rule.action === "external_directory" && rule.resource === SHELL_OUTPUT_GLOB && rule.effect === "deny",
+          )
+          if (
+            denied ||
+            PermissionV2.evaluate("external_directory", SHELL_OUTPUT_GLOB, agent.permissions).effect === "allow"
+          )
+            return
+          agent.permissions.push({ action: "external_directory", resource: SHELL_OUTPUT_GLOB, effect: "allow" })
+        })
+      }
     })
     yield* ctx.event.subscribe().pipe(
       Stream.filter((event) => event.type === "config.updated"),

packages/core/src/config/plugin/reference.ts

@@ -9,6 +9,8 @@ import { Reference } from "../../reference"
 import { AbsolutePath } from "../../schema"
 import { Global } from "../../global"
 import { Location } from "../../location"
+import { allowExternalDirectories } from "../../permission/defaults"
+import { Repository } from "../../repository"
 
 export const Plugin = define({
   id: "opencode.config.reference",
@@ -18,35 +20,20 @@ export const Plugin = define({
     const global = yield* Global.Service
     const loaded = { entries: yield* config.entries() }
     yield* ctx.reference.transform((draft) => {
-      const entries = new Map<string, Reference.Source>()
+      for (const [name, source] of sources(loaded.entries, location.directory, global.home)) draft.add(name, source)
-      for (const doc of loaded.entries.filter((entry): entry is Config.Document => entry.type === "document")) {
+    })
-        const directory = doc.path ? path.dirname(doc.path) : location.directory
+    yield* ctx.agent.transform((draft) => {
-        for (const [name, entry] of Object.entries(doc.info.references ?? {})) {
+      const permissions = allowExternalDirectories(
-          if (!validAlias(name)) continue
+        Array.from(sources(loaded.entries, location.directory, global.home)).flatMap(([, source]) => {
-          const description = typeof entry === "string" ? undefined : entry.description
+          if (source.type === "local") return [path.join(source.path, "*")]
-          const hidden = typeof entry === "string" ? undefined : entry.hidden
+          const repository = Repository.parse(source.repository)
-          entries.set(
+          if (!repository || !Repository.isRemote(repository)) return []
-            name,
+          return [path.join(Repository.cachePath(global.repos, repository), "*")]
-            local(entry)
+        }),
-              ? Reference.LocalSource.make({
+      )
-                  type: "local",
+      for (const current of draft.list()) {
-                  path: AbsolutePath.make(
+        draft.update(current.id, (agent) => agent.permissions.push(...permissions))
-                    localPath(directory, global.home, typeof entry === "string" ? entry : entry.path),
-                  ),
-                  ...(description === undefined ? {} : { description }),
-                  ...(hidden === undefined ? {} : { hidden }),
-                })
-              : Reference.GitSource.make({
-                  type: "git",
-                  repository: typeof entry === "string" ? entry : entry.repository,
-                  ...(entry.branch === undefined ? {} : { branch: entry.branch }),
-                  ...(description === undefined ? {} : { description }),
-                  ...(hidden === undefined ? {} : { hidden }),
-                }),
-          )
-        }
       }
-      for (const [name, source] of entries) draft.add(name, source)
     })
     yield* ctx.event.subscribe().pipe(
       Stream.filter((event) => event.type === "config.updated"),
@@ -54,6 +41,7 @@ export const Plugin = define({
         config.entries().pipe(
           Effect.tap((entries) => Effect.sync(() => (loaded.entries = entries))),
           Effect.andThen(ctx.reference.reload()),
+          Effect.andThen(ctx.agent.reload()),
         ),
       ),
       Effect.forkScoped({ startImmediately: true }),
@@ -61,6 +49,36 @@ export const Plugin = define({
   }),
 })
 
+function sources(entries: readonly Config.Entry[], location: string, home: string) {
+  const result = new Map<string, Reference.Source>()
+  for (const doc of entries.filter((entry): entry is Config.Document => entry.type === "document")) {
+    const directory = doc.path ? path.dirname(doc.path) : location
+    for (const [name, entry] of Object.entries(doc.info.references ?? {})) {
+      if (!validAlias(name)) continue
+      const description = typeof entry === "string" ? undefined : entry.description
+      const hidden = typeof entry === "string" ? undefined : entry.hidden
+      result.set(
+        name,
+        local(entry)
+          ? Reference.LocalSource.make({
+              type: "local",
+              path: AbsolutePath.make(localPath(directory, home, typeof entry === "string" ? entry : entry.path)),
+              ...(description === undefined ? {} : { description }),
+              ...(hidden === undefined ? {} : { hidden }),
+            })
+          : Reference.GitSource.make({
+              type: "git",
+              repository: typeof entry === "string" ? entry : entry.repository,
+              ...(entry.branch === undefined ? {} : { branch: entry.branch }),
+              ...(description === undefined ? {} : { description }),
+              ...(hidden === undefined ? {} : { hidden }),
+            }),
+      )
+    }
+  }
+  return result
+}
+
 function validAlias(name: string) {
   return name.length > 0 && !/[\/\s`,]/.test(name)
 }

packages/core/src/config/plugin/skill.ts

@@ -8,6 +8,8 @@ import { AbsolutePath } from "../../schema"
 import { SkillV2 } from "../../skill"
 import { Global } from "../../global"
 import { Location } from "../../location"
+import { SkillDiscovery } from "../../skill/discovery"
+import { allowExternalDirectories } from "../../permission/defaults"
 
 export const Plugin = define({
   id: "opencode.config.skill",
@@ -17,41 +19,19 @@ export const Plugin = define({
     const location = yield* Location.Service
     const loaded = { entries: yield* config.entries() }
     yield* ctx.skill.transform((draft) => {
-      const claude = loaded.entries.flatMap((entry) => (entry.type === "claude" ? [entry.path] : []))
+      for (const source of sources(loaded.entries, global.home, location.directory)) draft.source(source)
-      const agents = loaded.entries.flatMap((entry) => (entry.type === "agents" ? [entry.path] : []))
+    })
-      const directories = loaded.entries.flatMap((entry) => (entry.type === "directory" ? [entry.path] : []))
+    yield* ctx.agent.transform((draft) => {
-      const items = loaded.entries.flatMap((entry) => (entry.type === "document" ? (entry.info.skills ?? []) : []))
+      const permissions = allowExternalDirectories(
-      for (const directory of [...claude, ...agents]) {
+        sources(loaded.entries, global.home, location.directory).map((source) =>
-        draft.source(
+          path.join(
-          SkillV2.DirectorySource.make({
+            source.type === "directory" ? source.path : SkillDiscovery.cachePath(global.cache, source.url),
-            type: "directory",
+            "*",
-            path: AbsolutePath.make(path.join(directory, "skills")),
+          ),
-          }),
+        ),
-        )
+      )
-      }
+      for (const current of draft.list()) {
-      for (const directory of directories) {
+        draft.update(current.id, (agent) => agent.permissions.push(...permissions))
-        draft.source(
-          SkillV2.DirectorySource.make({ type: "directory", path: AbsolutePath.make(path.join(directory, "skill")) }),
-        )
-        draft.source(
-          SkillV2.DirectorySource.make({
-            type: "directory",
-            path: AbsolutePath.make(path.join(directory, "skills")),
-          }),
-        )
-      }
-      for (const item of items) {
-        if (URL.canParse(item) && /^(https?:)$/.test(new URL(item).protocol)) {
-          draft.source(SkillV2.UrlSource.make({ type: "url", url: item }))
-          continue
-        }
-        const expanded = item.startsWith("~/") ? path.join(global.home, item.slice(2)) : item
-        draft.source(
-          SkillV2.DirectorySource.make({
-            type: "directory",
-            path: AbsolutePath.make(path.isAbsolute(expanded) ? expanded : path.join(location.directory, expanded)),
-          }),
-        )
       }
     })
     yield* ctx.event.subscribe().pipe(
@@ -60,9 +40,44 @@ export const Plugin = define({
         config.entries().pipe(
           Effect.tap((entries) => Effect.sync(() => (loaded.entries = entries))),
           Effect.andThen(ctx.skill.reload()),
+          Effect.andThen(ctx.agent.reload()),
         ),
       ),
       Effect.forkScoped({ startImmediately: true }),
     )
   }),
 })
+
+function sources(entries: readonly Config.Entry[], home: string, directory: string) {
+  const result: Array<SkillV2.DirectorySource | SkillV2.UrlSource> = []
+  for (const entry of entries) {
+    if (entry.type === "claude" || entry.type === "agents") {
+      result.push(
+        SkillV2.DirectorySource.make({ type: "directory", path: AbsolutePath.make(path.join(entry.path, "skills")) }),
+      )
+      continue
+    }
+    if (entry.type === "directory") {
+      result.push(
+        SkillV2.DirectorySource.make({ type: "directory", path: AbsolutePath.make(path.join(entry.path, "skill")) }),
+        SkillV2.DirectorySource.make({ type: "directory", path: AbsolutePath.make(path.join(entry.path, "skills")) }),
+      )
+      continue
+    }
+    if (entry.type !== "document") continue
+    for (const item of entry.info.skills ?? []) {
+      if (URL.canParse(item) && /^(https?:)$/.test(new URL(item).protocol)) {
+        result.push(SkillV2.UrlSource.make({ type: "url", url: item }))
+        continue
+      }
+      const expanded = item.startsWith("~/") ? path.join(home, item.slice(2)) : item
+      result.push(
+        SkillV2.DirectorySource.make({
+          type: "directory",
+          path: AbsolutePath.make(path.isAbsolute(expanded) ? expanded : path.join(directory, expanded)),
+        }),
+      )
+    }
+  }
+  return result
+}

packages/core/src/permission/defaults.ts

@@ -0,0 +1,10 @@
+import path from "path"
+import { Global } from "../global"
+import { PermissionV2 } from "../permission"
+
+// Combined output files written by the Shell service, e.g. `<data>/shell/<projectID>/<shellID>.out`.
+export const SHELL_OUTPUT_GLOB = path.join(Global.Path.data, "shell", "*", "*")
+
+export function allowExternalDirectories(resources: readonly string[]): PermissionV2.Ruleset {
+  return resources.map((resource): PermissionV2.Rule => ({ action: "external_directory", resource, effect: "allow" }))
+}

packages/core/src/plugin/agent.ts

@@ -7,10 +7,8 @@ import { AgentV2 } from "../agent"
 import { Global } from "../global"
 import { Location } from "../location"
 import { PermissionV2 } from "../permission"
+import { SHELL_OUTPUT_GLOB } from "../permission/defaults"
 
-// Combined output files written by the Shell service, e.g. `<data>/shell/<projectID>/<shellID>.out`.
-// Whitelisted so agents can read a command's full captured output without an external-directory prompt.
-const SHELL_OUTPUT_GLOB = path.join(Global.Path.data, "shell", "*", "*")
 const BUILD_SYSTEM =
   "You are an AI coding agent. Help the user accomplish software engineering tasks by inspecting the workspace, making targeted changes, and using tools according to the configured permissions."
 

packages/core/src/plugin/internal.ts

@@ -147,9 +147,9 @@ const pre = [
 
 const post = [
   ConfigReferencePlugin.Plugin,
+  ConfigSkillPlugin.Plugin,
   ConfigAgentPlugin.Plugin,
   ConfigCommandPlugin.Plugin,
-  ConfigSkillPlugin.Plugin,
   ConfigProviderPlugin.Plugin,
   VariantPlugin.Plugin,
   ConfigPolicyPlugin.Plugin,

packages/core/src/skill/discovery.ts

@@ -69,6 +69,10 @@ export interface Interface {
 
 export class Service extends Context.Service<Service, Interface>()("@opencode/v2/SkillDiscovery") {}
 
+export function cachePath(cache: string, url: string) {
+  return path.resolve(cache, "skills", Hash.fast(url.endsWith("/") ? url : `${url}/`))
+}
+
 const layer = Layer.effect(
   Service,
   Effect.gen(function* () {
@@ -111,7 +115,7 @@ const layer = Layer.effect(
         )
         if (!data) return []
 
-        const sourceRoot = path.resolve(global.cache, "skills", Hash.fast(base))
+        const sourceRoot = cachePath(global.cache, base)
         return yield* Effect.forEach(
           data.skills.flatMap((skill) => {
             if (!isSafeSegment(skill.name)) {

packages/core/test/config/agent.test.ts

@@ -10,6 +10,7 @@ import { LayerNode } from "@opencode-ai/core/effect/layer-node"
 import { FSUtil } from "@opencode-ai/core/fs-util"
 import { Global } from "@opencode-ai/core/global"
 import { PermissionV2 } from "@opencode-ai/core/permission"
+import { SHELL_OUTPUT_GLOB } from "@opencode-ai/core/permission/defaults"
 import { AbsolutePath } from "@opencode-ai/core/schema"
 import { ConfigMigrateV1 } from "@opencode-ai/core/v1/config/migrate"
 import { tmpdir } from "../fixture/tmpdir"
@@ -22,6 +23,11 @@ const defaultPermissions = [
   { action: "*", resource: "*", effect: "allow" },
   { action: "external_directory", resource: "*", effect: "ask" },
 ] satisfies PermissionV2.Ruleset
+const shellOutputPermission = {
+  action: "external_directory",
+  resource: SHELL_OUTPUT_GLOB,
+  effect: "allow",
+} satisfies PermissionV2.Rule
 
 describe("ConfigAgentPlugin.Plugin", () => {
   it.effect("matches POSIX paths against home-relative permissions", () =>
@@ -114,6 +120,7 @@ describe("ConfigAgentPlugin.Plugin", () => {
         { action: "bash", resource: "*", effect: "ask" },
         { action: "read", resource: "*", effect: "allow" },
         { action: "bash", resource: "git *", effect: "allow" },
+        shellOutputPermission,
       ])
       expect(PermissionV2.evaluate("bash", "git status", buildAgent.permissions).effect).toBe("allow")
       expect(PermissionV2.evaluate("bash", "bun test", buildAgent.permissions).effect).toBe("ask")
@@ -132,6 +139,7 @@ describe("ConfigAgentPlugin.Plugin", () => {
         { action: "read", resource: "*", effect: "allow" },
         { action: "edit", resource: "*", effect: "deny" },
         { action: "read", resource: "*", effect: "deny" },
+        shellOutputPermission,
       ])
       expect(PermissionV2.evaluate("read", "README.md", reviewer.permissions).effect).toBe("deny")
       expect((yield* agents.get(AgentV2.ID.make("late")))?.permissions).toEqual([
@@ -139,11 +147,31 @@ describe("ConfigAgentPlugin.Plugin", () => {
         { action: "bash", resource: "*", effect: "ask" },
         { action: "read", resource: "*", effect: "allow" },
         { action: "edit", resource: "*", effect: "allow" },
+        shellOutputPermission,
       ])
       expect(yield* agents.get(AgentV2.ID.make("removed"))).toBeUndefined()
     }),
   )
 
+  it.effect("keeps shell output readable through a broad external-directory deny", () =>
+    Effect.gen(function* () {
+      const permissions = yield* loadConfiguredPermissions([
+        { action: "external_directory", resource: "*", effect: "deny" },
+      ])
+      expect(PermissionV2.evaluate("external_directory", SHELL_OUTPUT_GLOB, permissions).effect).toBe("allow")
+    }),
+  )
+
+  it.effect("respects an exact shell output deny", () =>
+    Effect.gen(function* () {
+      const permissions = yield* loadConfiguredPermissions([
+        { action: "external_directory", resource: "*", effect: "deny" },
+        { action: "external_directory", resource: SHELL_OUTPUT_GLOB, effect: "deny" },
+      ])
+      expect(PermissionV2.evaluate("external_directory", SHELL_OUTPUT_GLOB, permissions).effect).toBe("deny")
+    }),
+  )
+
   it.effect("maps configured agent fields and preserves an unspecified model variant", () =>
     Effect.gen(function* () {
       const agents = yield* AgentV2.Service
@@ -294,13 +322,21 @@ Use native v2 fields.`,
             system: "Review carefully.",
             description: "Markdown description",
             request: { body: { temperature: 0.5 } },
-            permissions: [...defaultPermissions, { action: "edit", resource: "*", effect: "deny" }],
+            permissions: [
+              ...defaultPermissions,
+              { action: "edit", resource: "*", effect: "deny" },
+              shellOutputPermission,
+            ],
           })
           expect(yield* agents.get(AgentV2.ID.make("team/helper"))).toMatchObject({ system: "Help the team." })
           expect(yield* agents.get(AgentV2.ID.make("native"))).toMatchObject({
             system: "Use native v2 fields.",
             request: { headers: { "x-agent": "native" }, body: { effort: "high" } },
-            permissions: [...defaultPermissions, { action: "edit", resource: "*", effect: "deny" }],
+            permissions: [
+              ...defaultPermissions,
+              { action: "edit", resource: "*", effect: "deny" },
+              shellOutputPermission,
+            ],
           })
           expect(yield* agents.get(AgentV2.ID.make("disabled"))).toBeUndefined()
           expect(yield* agents.get(AgentV2.ID.make("plan"))).toMatchObject({ system: "Make a plan.", mode: "primary" })
@@ -357,3 +393,26 @@ function loadHomePermissions(home: string) {
     return agent.permissions
   })
 }
+
+function loadConfiguredPermissions(permissions: PermissionV2.Ruleset) {
+  return Effect.gen(function* () {
+    const agents = yield* AgentV2.Service
+    const build = AgentV2.ID.make("build")
+    yield* agents.transform((draft) => draft.update(build, () => {}))
+    const config = Config.Service.of({
+      entries: () =>
+        Effect.succeed([
+          new Config.Document({
+            type: "document",
+            info: decode({ permissions }),
+          }),
+        ]),
+    })
+    yield* ConfigAgentPlugin.Plugin.effect(host({ agent: agentHost(agents) })).pipe(
+      Effect.provideService(Config.Service, config),
+    )
+    const agent = yield* agents.get(build)
+    if (!agent) throw new Error("expected configured build agent")
+    return agent.permissions
+  })
+}

packages/core/test/config/skill.test.ts

@@ -34,8 +34,10 @@ describe("ConfigSkillPlugin.Plugin", () => {
         return { dispose }
       })
 
+      const agent = host().agent
       yield* ConfigSkillPlugin.Plugin.effect(
         host({
+          agent: { ...agent, transform: () => Effect.succeed({ dispose: Effect.void }) },
           skill: { list: () => Effect.die("unused skill.list"), transform, reload: () => Effect.void },
         }),
       ).pipe(

packages/core/test/location-layer.test.ts

@@ -18,6 +18,7 @@ import { PluginSupervisor } from "@opencode-ai/core/plugin/supervisor"
 import { ModelV2 } from "@opencode-ai/core/model"
 import { ProjectV2 } from "@opencode-ai/core/project"
 import { ProviderV2 } from "@opencode-ai/core/provider"
+import { PermissionV2 } from "@opencode-ai/core/permission"
 import { AbsolutePath } from "@opencode-ai/core/schema"
 import { SessionV2 } from "@opencode-ai/core/session"
 import { SessionRunnerModel } from "@opencode-ai/core/session/runner/model"
@@ -112,6 +113,70 @@ describe("LocationServiceMap", () => {
     ),
   )
 
+  it.live("allows external skill and reference directories by default", () =>
+    Effect.acquireRelease(
+      Effect.promise(() => Promise.all([tmpdir(), tmpdir()])),
+      (dirs) => Effect.promise(() => Promise.all(dirs.map((dir) => dir[Symbol.asyncDispose]())).then(() => undefined)),
+    ).pipe(
+      Effect.flatMap(([project, external]) =>
+        Effect.gen(function* () {
+          const skill = path.join(external.path, "skills", "example")
+          const reference = path.join(external.path, "reference")
+          yield* Effect.promise(() =>
+            Promise.all([
+              fs.mkdir(skill, { recursive: true }),
+              fs.mkdir(reference, { recursive: true }),
+              fs.writeFile(
+                path.join(project.path, "opencode.json"),
+                JSON.stringify({
+                  skills: [path.join(external.path, "skills")],
+                  references: { docs: reference },
+                }),
+              ),
+            ]),
+          )
+          yield* Effect.promise(() =>
+            fs.writeFile(
+              path.join(skill, "SKILL.md"),
+              "---\nname: example\ndescription: Example skill.\n---\n\n# Example\n",
+            ),
+          )
+
+          const locations = yield* LocationServiceMap.Service
+          const context = locations.get(Location.Ref.make({ directory: AbsolutePath.make(project.path) }))
+          const permissions = yield* Effect.gen(function* () {
+            const supervisor = yield* PluginSupervisor.Service
+            const agents = yield* AgentV2.Service
+            yield* supervisor.flush
+            for (let attempt = 0; attempt < 100; attempt++) {
+              const build = yield* agents.resolve("build")
+              if (
+                build &&
+                PermissionV2.evaluate(
+                  "external_directory",
+                  path.join(skill, "reference", "notes.md"),
+                  build.permissions,
+                ).effect === "allow" &&
+                PermissionV2.evaluate("external_directory", path.join(reference, "notes.md"), build.permissions)
+                  .effect === "allow"
+              )
+                return build.permissions
+              yield* Effect.sleep("20 millis")
+            }
+            return (yield* agents.resolve("build"))?.permissions ?? []
+          }).pipe(Effect.scoped, Effect.provide(context))
+
+          expect(
+            PermissionV2.evaluate("external_directory", path.join(skill, "reference", "notes.md"), permissions).effect,
+          ).toBe("allow")
+          expect(
+            PermissionV2.evaluate("external_directory", path.join(reference, "notes.md"), permissions).effect,
+          ).toBe("allow")
+        }),
+      ),
+    ),
+  )
+
   itWithSdk.live("reruns activation for SDK plugins registered during startup", () =>
     Effect.acquireRelease(
       Effect.promise(() => tmpdir()),