permissions: move workspace roots onto thread state

codex-rs/app-server-protocol/schema/json/v2/ThreadResumeParams.json

@@ -298,65 +298,6 @@
         }
       ]
     },
-    "PermissionProfileModificationParams": {
-      "oneOf": [
-        {
-          "description": "Additional concrete directory that should be writable.",
-          "properties": {
-            "path": {
-              "$ref": "#/definitions/AbsolutePathBuf"
-            },
-            "type": {
-              "enum": [
-                "additionalWritableRoot"
-              ],
-              "title": "AdditionalWritableRootPermissionProfileModificationParamsType",
-              "type": "string"
-            }
-          },
-          "required": [
-            "path",
-            "type"
-          ],
-          "title": "AdditionalWritableRootPermissionProfileModificationParams",
-          "type": "object"
-        }
-      ]
-    },
-    "PermissionProfileSelectionParams": {
-      "oneOf": [
-        {
-          "description": "Select a named built-in or user-defined profile and optionally apply bounded modifications that Codex knows how to validate.",
-          "properties": {
-            "id": {
-              "type": "string"
-            },
-            "modifications": {
-              "items": {
-                "$ref": "#/definitions/PermissionProfileModificationParams"
-              },
-              "type": [
-                "array",
-                "null"
-              ]
-            },
-            "type": {
-              "enum": [
-                "profile"
-              ],
-              "title": "ProfilePermissionProfileSelectionParamsType",
-              "type": "string"
-            }
-          },
-          "required": [
-            "id",
-            "type"
-          ],
-          "title": "ProfilePermissionProfileSelectionParams",
-          "type": "object"
-        }
-      ]
-    },
     "Personality": {
       "enum": [
         "none",
@@ -1091,7 +1032,8 @@
         {
           "type": "null"
         }
-      ]
+      ],
+      "description": "Deprecated for resume. When present, the server treats this as a compatibility spelling for selecting a matching named permissions profile."
     },
     "serviceTier": {
       "type": [