fix: preserve permission ordering by accepting a layered array

packages/opencode/src/agent/agent.ts

@@ -1,4 +1,5 @@
 import { Config } from "@/config/config"
+import { ConfigPermission } from "@/config/permission"
 import { Provider } from "@/provider/provider"
 import { ModelID, ProviderID } from "../provider/schema"
 import { generateObject, streamObject, type ModelMessage } from "ai"
@@ -116,7 +117,10 @@ export const layer = Layer.effect(
           },
         })
 
-        const user = Permission.fromConfig(cfg.permission ?? {})
+        // Convert permission layers to rulesets and merge them
+        // Each layer's rules come after the previous, so later configs override earlier ones
+        const layers = ConfigPermission.toLayers(cfg.permission)
+        const user = Permission.merge(...layers.map((p) => Permission.fromConfig(p)))
 
         const agents: Record<string, Info> = {
           build: {

packages/opencode/src/config/config.ts

@@ -56,6 +56,13 @@ function mergeConfigConcatArrays(target: Info, source: Info): Info {
   if (target.instructions && source.instructions) {
     merged.instructions = Array.from(new Set([...target.instructions, ...source.instructions]))
   }
+  // Accumulate permission layers for later merging as rulesets.
+  // This preserves the ordering semantics: later rules override earlier rules.
+  // Each layer keeps the raw shape the user wrote on disk; consumers should use
+  // ConfigPermission.toLayers to normalise.
+  if (source.permission) {
+    merged.permission = [...ConfigPermission.toLayers(target.permission), ...ConfigPermission.toLayers(source.permission)]
+  }
   return merged
 }
 
@@ -229,7 +236,12 @@ export const Info = Schema.Struct({
     description: "Additional instruction files or patterns to include",
   }),
   layout: Schema.optional(ConfigLayout.Layout).annotate({ description: "@deprecated Always uses stretch layout." }),
-  permission: Schema.optional(ConfigPermission.Info),
+  permission: Schema.optional(
+    Schema.Union([ConfigPermission.Info, Schema.mutable(Schema.Array(ConfigPermission.Info))]),
+  ).annotate({
+    description:
+      "Permission configuration. Accepts a single object (per-tool action map) or an array of layered configs; arrays are merged in order so later layers override earlier ones.",
+  }),
   tools: Schema.optional(Schema.Record(Schema.String, Schema.Boolean)),
   attachment: Schema.optional(ConfigAttachment.Info).annotate({
     description: "Attachment processing configuration, including image size limits and resizing behavior",
@@ -708,11 +720,12 @@ export const layer = Layer.effect(
         }
 
         if (Flag.OPENCODE_PERMISSION) {
-          result.permission = mergeDeep(result.permission ?? {}, JSON.parse(Flag.OPENCODE_PERMISSION))
+          const envPermission = JSON.parse(Flag.OPENCODE_PERMISSION) as ConfigPermission.Info
+          result.permission = [...ConfigPermission.toLayers(result.permission), envPermission]
         }
 
         if (result.tools) {
-          const perms: Record<string, ConfigPermission.Action> = {}
+          const perms: ConfigPermission.Info = {}
           for (const [tool, enabled] of Object.entries(result.tools)) {
             const action: ConfigPermission.Action = enabled ? "allow" : "deny"
             if (tool === "write" || tool === "edit" || tool === "patch") {
@@ -721,7 +734,8 @@ export const layer = Layer.effect(
             }
             perms[tool] = action
           }
-          result.permission = mergeDeep(perms, result.permission ?? {})
+          // Tools permissions come before other permissions (they can be overridden)
+          result.permission = [perms, ...ConfigPermission.toLayers(result.permission)]
         }
 
         if (!result.username) result.username = os.userInfo().username

packages/opencode/src/config/permission.ts

@@ -57,3 +57,11 @@ export const Info = InputSchema.pipe(
 ).annotate({ identifier: "PermissionConfig" })
 type _Info = Schema.Schema.Type<typeof InputObject>
 export type Info = { -readonly [K in keyof _Info]: _Info[K] }
+
+// Top-level config accepts either a single permission object or an array of
+// layered configs. Internal merging produces arrays; this helper normalises
+// either shape into the array form expected by consumers.
+export function toLayers(value: Info | Info[] | undefined): Info[] {
+  if (!value) return []
+  return Array.isArray(value) ? value : [value]
+}

packages/opencode/test/config/config.test.ts

@@ -3,7 +3,9 @@ import { Effect, Layer, Option } from "effect"
 import { NodeFileSystem, NodePath } from "@effect/platform-node"
 import { Config } from "@/config/config"
 import { ConfigManaged } from "@/config/managed"
+import { ConfigPermission } from "@/config/permission"
 import { ConfigParse } from "../../src/config/parse"
+import { Permission } from "../../src/permission"
 import { EffectFlock } from "@opencode-ai/core/util/effect-flock"
 
 import { Instance } from "../../src/project/instance"
@@ -276,6 +278,40 @@ test("updates global config and omits empty shell key in json", async () => {
   }
 })
 
+test("global config update preserves single-object permission shape on disk", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          shell: "bash",
+          permission: { bash: "ask" },
+        }),
+      )
+    },
+  })
+
+  const prev = Global.Path.config
+  ;(Global.Path as { config: string }).config = tmp.path
+  await clear(true)
+
+  try {
+    // Updating an unrelated key must not rewrite `permission` from object to array form.
+    await saveGlobal({ shell: "zsh" })
+
+    const written = await Filesystem.readJson<{ permission?: unknown; shell?: string }>(
+      path.join(tmp.path, "opencode.json"),
+    )
+    expect(written.shell).toBe("zsh")
+    expect(Array.isArray(written.permission)).toBe(false)
+    expect(written.permission).toEqual({ bash: "ask" })
+  } finally {
+    ;(Global.Path as { config: string }).config = prev
+    await clear(true)
+  }
+})
+
 test("updates global config and omits empty shell key in jsonc", async () => {
   await using tmp = await tmpdir({
     init: async (dir) => {
@@ -1713,7 +1749,10 @@ test("permission config preserves user key order", async () => {
     directory: tmp.path,
     fn: async () => {
       const config = await load()
-      expect(Object.keys(config.permission!)).toEqual([
+      // load() goes through the merge pipeline, producing the layered array form
+      expect(config.permission).toHaveLength(1)
+      const perm = (config.permission as ConfigPermission.Info[])[0]
+      expect(Object.keys(perm)).toEqual([
         "*",
         "edit",
         "write",
@@ -1729,6 +1768,129 @@ test("permission config preserves user key order", async () => {
   })
 })
 
+// Global bash "rm *" deny is inherited, but user's top-level "*" ask comes after and overrides it
+test("user top-level catchall overrides inherited bash rules", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          permission: {
+            bash: { "rm *": "deny" },
+          },
+        }),
+      )
+      const opencodeDir = path.join(dir, ".opencode")
+      await fs.mkdir(opencodeDir, { recursive: true })
+      await Filesystem.write(
+        path.join(opencodeDir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          permission: {
+            "*": "ask",
+            bash: { "ls *": "allow" },
+          },
+        }),
+      )
+    },
+  })
+  await WithInstance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await load()
+      const layers = ConfigPermission.toLayers(config.permission)
+      const ruleset = Permission.merge(...layers.map((p) => Permission.fromConfig(p)))
+
+      expect(Permission.evaluate("bash", "rm -rf /", ruleset).action).toBe("ask")
+      expect(Permission.evaluate("bash", "ls -la", ruleset).action).toBe("allow")
+      expect(Permission.evaluate("bash", "echo hello", ruleset).action).toBe("ask")
+    },
+  })
+})
+
+// No top-level catchall, so global bash "rm *" deny is preserved
+test("inherited bash rules apply when no user top-level catchall", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          permission: {
+            bash: { "rm *": "deny" },
+          },
+        }),
+      )
+      const opencodeDir = path.join(dir, ".opencode")
+      await fs.mkdir(opencodeDir, { recursive: true })
+      await Filesystem.write(
+        path.join(opencodeDir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          permission: {
+            bash: { "ls *": "allow" },
+          },
+        }),
+      )
+    },
+  })
+  await WithInstance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await load()
+      const layers = ConfigPermission.toLayers(config.permission)
+      const ruleset = Permission.merge(...layers.map((p) => Permission.fromConfig(p)))
+
+      expect(Permission.evaluate("bash", "rm -rf /", ruleset).action).toBe("deny")
+      expect(Permission.evaluate("bash", "ls -la", ruleset).action).toBe("allow")
+    },
+  })
+})
+
+// User's bash "*" catchall overrides global "rm *" deny
+test("user bash catchall overrides inherited bash rules", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Filesystem.write(
+        path.join(dir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          permission: {
+            bash: { "rm *": "deny" },
+          },
+        }),
+      )
+      const opencodeDir = path.join(dir, ".opencode")
+      await fs.mkdir(opencodeDir, { recursive: true })
+      await Filesystem.write(
+        path.join(opencodeDir, "opencode.json"),
+        JSON.stringify({
+          $schema: "https://opencode.ai/config.json",
+          permission: {
+            bash: { "*": "ask", "ls *": "allow" },
+          },
+        }),
+      )
+    },
+  })
+  await WithInstance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await load()
+      const layers = ConfigPermission.toLayers(config.permission)
+      const ruleset = Permission.merge(...layers.map((p) => Permission.fromConfig(p)))
+
+      expect(Permission.evaluate("bash", "rm -rf /", ruleset).action).toBe("ask")
+      expect(Permission.evaluate("bash", "ls -la", ruleset).action).toBe("allow")
+      expect(Permission.evaluate("bash", "echo hello", ruleset).action).toBe("ask")
+
+      // Non-bash permissions should use the top-level "*" rule
+      expect(Permission.evaluate("read", "foo.txt", ruleset).action).toBe("ask")
+    },
+  })
+})
+
 test("config parser preserves permission order while rejecting unknown top-level keys", () => {
   const config = ConfigParse.schema(
     Config.Info,
@@ -1742,7 +1904,8 @@ test("config parser preserves permission order while rejecting unknown top-level
     "test",
   )
 
-  expect(Object.keys(config.permission!)).toEqual(["bash", "*", "edit"])
+  // ConfigParse.schema preserves the raw shape the user wrote
+  expect(Object.keys(config.permission as ConfigPermission.Info)).toEqual(["bash", "*", "edit"])
   try {
     ConfigParse.schema(Config.Info, { invalid_field: true }, "test")
     throw new Error("expected config parse to fail")
@@ -2579,11 +2742,12 @@ test("parseManagedPlist parses permission rules", async () => {
     ),
     "test:mobileconfig",
   )
-  expect(config.permission?.["*"]).toBe("ask")
-  expect(config.permission?.grep).toBe("allow")
-  expect(config.permission?.webfetch).toBe("ask")
-  expect(config.permission?.["~/.ssh/*"]).toBe("deny")
-  const bash = config.permission?.bash as Record<string, string>
+  const perm = config.permission as ConfigPermission.Info
+  expect(perm?.["*"]).toBe("ask")
+  expect(perm?.grep).toBe("allow")
+  expect(perm?.webfetch).toBe("ask")
+  expect(perm?.["~/.ssh/*"]).toBe("deny")
+  const bash = perm?.bash as Record<string, string>
   expect(bash?.["rm -rf *"]).toBe("deny")
   expect(bash?.["curl *"]).toBe("deny")
 })

packages/opencode/test/permission-task.test.ts

@@ -1,6 +1,7 @@
 import { afterEach, describe, test, expect } from "bun:test"
 import { Permission } from "../src/permission"
 import { Config } from "@/config/config"
+import { ConfigPermission } from "@/config/permission"
 import { Instance } from "../src/project/instance"
 import { WithInstance } from "../src/project/with-instance"
 import { disposeAllInstances, tmpdir } from "./fixture/fixture"
@@ -163,7 +164,9 @@ describe("permission.task with real config files", () => {
       directory: tmp.path,
       fn: async () => {
         const config = await load()
-        const ruleset = Permission.fromConfig(config.permission ?? {})
+        const ruleset = Permission.merge(
+          ...ConfigPermission.toLayers(config.permission).map((p) => Permission.fromConfig(p)),
+        )
         // general and orchestrator-fast should be allowed, code-reviewer denied
         expect(Permission.evaluate("task", "general", ruleset).action).toBe("allow")
         expect(Permission.evaluate("task", "orchestrator-fast", ruleset).action).toBe("allow")
@@ -188,7 +191,9 @@ describe("permission.task with real config files", () => {
       directory: tmp.path,
       fn: async () => {
         const config = await load()
-        const ruleset = Permission.fromConfig(config.permission ?? {})
+        const ruleset = Permission.merge(
+          ...ConfigPermission.toLayers(config.permission).map((p) => Permission.fromConfig(p)),
+        )
         // general and code-reviewer should be ask, orchestrator-* denied
         expect(Permission.evaluate("task", "general", ruleset).action).toBe("ask")
         expect(Permission.evaluate("task", "code-reviewer", ruleset).action).toBe("ask")
@@ -213,7 +218,9 @@ describe("permission.task with real config files", () => {
       directory: tmp.path,
       fn: async () => {
         const config = await load()
-        const ruleset = Permission.fromConfig(config.permission ?? {})
+        const ruleset = Permission.merge(
+          ...ConfigPermission.toLayers(config.permission).map((p) => Permission.fromConfig(p)),
+        )
         expect(Permission.evaluate("task", "general", ruleset).action).toBe("allow")
         expect(Permission.evaluate("task", "code-reviewer", ruleset).action).toBe("deny")
         // Unspecified agents default to "ask"
@@ -240,7 +247,9 @@ describe("permission.task with real config files", () => {
       directory: tmp.path,
       fn: async () => {
         const config = await load()
-        const ruleset = Permission.fromConfig(config.permission ?? {})
+        const ruleset = Permission.merge(
+          ...ConfigPermission.toLayers(config.permission).map((p) => Permission.fromConfig(p)),
+        )
 
         // Verify task permissions
         expect(Permission.evaluate("task", "general", ruleset).action).toBe("allow")
@@ -278,7 +287,9 @@ describe("permission.task with real config files", () => {
       directory: tmp.path,
       fn: async () => {
         const config = await load()
-        const ruleset = Permission.fromConfig(config.permission ?? {})
+        const ruleset = Permission.merge(
+          ...ConfigPermission.toLayers(config.permission).map((p) => Permission.fromConfig(p)),
+        )
 
         // Last matching rule wins - "*" deny is last, so all agents are denied
         expect(Permission.evaluate("task", "general", ruleset).action).toBe("deny")
@@ -309,7 +320,9 @@ describe("permission.task with real config files", () => {
       directory: tmp.path,
       fn: async () => {
         const config = await load()
-        const ruleset = Permission.fromConfig(config.permission ?? {})
+        const ruleset = Permission.merge(
+          ...ConfigPermission.toLayers(config.permission).map((p) => Permission.fromConfig(p)),
+        )
 
         // Evaluate uses findLast - "general" allow comes after "*" deny
         expect(Permission.evaluate("task", "general", ruleset).action).toBe("allow")