fix: preserve permission ordering by accepting a layered array (#23214)

Co-authored-by: Andrew Suffield <asuffield@cloudflare.com>
Co-authored-by: Aiden Cline <aidenpcline@gmail.com>

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"
@@ -117,7 +118,10 @@ 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

@@ -55,6 +55,13 @@ 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
 }
 
@@ -228,7 +235,12 @@ 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",
@@ -704,11 +716,12 @@ 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") {
@@ -717,7 +730,8 @@ 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

@@ -56,3 +56,11 @@ 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]
+}