tui: add development scripts for better debugging workflow

packages/opencode/package.json

@@ -26,6 +26,7 @@
   "devDependencies": {
     "@babel/core": "7.28.4",
     "@octokit/webhooks-types": "7.6.1",
+    "@opencode-ai/script": "workspace:*",
     "@parcel/watcher-darwin-arm64": "2.5.1",
     "@parcel/watcher-darwin-x64": "2.5.1",
     "@parcel/watcher-linux-arm64-glibc": "2.5.1",
@@ -39,12 +40,11 @@
     "@types/bun": "catalog:",
     "@types/turndown": "5.0.5",
     "@types/yargs": "17.0.33",
-    "typescript": "catalog:",
     "@typescript/native-preview": "catalog:",
+    "typescript": "catalog:",
     "vscode-languageserver-types": "3.17.5",
     "why-is-node-running": "3.2.2",
-    "zod-to-json-schema": "3.24.5",
-    "@opencode-ai/script": "workspace:*"
+    "zod-to-json-schema": "3.24.5"
   },
   "dependencies": {
     "@actions/core": "1.11.1",

packages/opencode/src/config/config.ts

@@ -480,7 +480,7 @@ export namespace Config {
       }
 
       // Convert legacy tools config to permissions
-      const permission: Permission = { ...agent.permission }
+      const permission: Permission = {}
       for (const [tool, enabled] of Object.entries(agent.tools ?? {})) {
         const action = enabled ? "allow" : "deny"
         // write, edit, patch, multiedit all map to edit permission
@@ -490,6 +490,7 @@ export namespace Config {
           permission[tool] = action
         }
       }
+      Object.assign(permission, agent.permission)
 
       // Convert legacy maxSteps to steps
       const steps = agent.steps ?? agent.maxSteps