fix(agents): clear stale frontier tool denies

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/agents/builtin-agents/hephaestus-agent.ts

@@ -8,7 +8,7 @@ import { applyEnvironmentContext } from "./environment-context"
 import { applyCategoryOverride, mergeAgentConfig } from "./agent-overrides"
 import { applyModelResolution, getFirstFallbackModel } from "./model-resolution"
 import { getGptApplyPatchPermission } from "../gpt-apply-patch-guard"
-import { getFrontierToolSchemaPermission } from "../frontier-tool-schema-guard"
+import { applyFrontierToolSchemaPermission } from "../frontier-tool-schema-guard"
 
 export function maybeCreateHephaestusConfig(input: {
   disabledAgents: string[]
@@ -90,10 +90,11 @@ export function maybeCreateHephaestusConfig(input: {
   }
 
   const resolvedModel = hephaestusConfig.model ?? ""
-  const frontierDeny = getFrontierToolSchemaPermission(resolvedModel)
-  if (Object.keys(frontierDeny).length > 0 && hephaestusConfig.permission) {
-    Object.assign(hephaestusConfig.permission, frontierDeny)
-  }
+  hephaestusConfig.permission = applyFrontierToolSchemaPermission(
+    hephaestusConfig.permission,
+    resolvedModel,
+    hephaestusOverride?.permission
+  )
 
   const gptDeny = getGptApplyPatchPermission(resolvedModel)
   if (Object.keys(gptDeny).length > 0 && hephaestusConfig.permission) {

src/agents/builtin-agents/sisyphus-agent.test.ts

@@ -143,6 +143,75 @@ describe("maybeCreateSisyphusConfig", () => {
     });
   });
 
+  describe("#given frontier default model with category override to non-frontier model", () => {
+    test("#when config is created #then stale grep and glob denies are cleared", () => {
+      // given
+      const agentOverrides: AgentOverrides = {
+        sisyphus: {
+          category: "non-frontier",
+        },
+      };
+      const mergedCategories: Record<string, CategoryConfig> = {
+        "non-frontier": {
+          model: "openai/gpt-5.4",
+        },
+      };
+
+      // when
+      const config = maybeCreateSisyphusConfig({
+        disabledAgents: [],
+        agentOverrides,
+        availableModels: new Set(["anthropic/claude-opus-4-7", "openai/gpt-5.4"]),
+        systemDefaultModel: "anthropic/claude-opus-4-7",
+        isFirstRunNoCache: false,
+        availableAgents: [],
+        availableSkills: [],
+        availableCategories: [],
+        mergedCategories,
+        useTaskSystem: false,
+      });
+
+      // then
+      expect(config?.model).toBe("openai/gpt-5.4");
+      expect(config?.permission).not.toHaveProperty("grep");
+      expect(config?.permission).not.toHaveProperty("glob");
+    });
+  });
+
+  describe("#given non-frontier model with user override denying grep and glob", () => {
+    test("#when config is created #then explicit user denies are preserved", () => {
+      // given
+      const agentOverrides: AgentOverrides = {
+        sisyphus: {
+          model: "openai/gpt-5.4",
+          permission: {
+            grep: "deny",
+            glob: "deny",
+          } as Record<string, "deny">,
+        },
+      };
+      const mergedCategories: Record<string, CategoryConfig> = {};
+
+      // when
+      const config = maybeCreateSisyphusConfig({
+        disabledAgents: [],
+        agentOverrides,
+        availableModels: new Set(["openai/gpt-5.4"]),
+        systemDefaultModel: "openai/gpt-5.4",
+        isFirstRunNoCache: false,
+        availableAgents: [],
+        availableSkills: [],
+        availableCategories: [],
+        mergedCategories,
+        useTaskSystem: false,
+      });
+
+      // then
+      expect(config?.permission).toHaveProperty("grep", "deny");
+      expect(config?.permission).toHaveProperty("glob", "deny");
+    });
+  });
+
   describe("#given generic GPT model with user override allowing apply_patch", () => {
     test("#when config is created #then apply_patch is still denied", () => {
       // given

src/agents/builtin-agents/sisyphus-agent.ts

@@ -8,7 +8,7 @@ import { applyOverrides } from "./agent-overrides"
 import { applyModelResolution, getFirstFallbackModel } from "./model-resolution"
 import { createSisyphusAgent } from "../sisyphus"
 import { getGptApplyPatchPermission } from "../gpt-apply-patch-guard"
-import { getFrontierToolSchemaPermission } from "../frontier-tool-schema-guard"
+import { applyFrontierToolSchemaPermission } from "../frontier-tool-schema-guard"
 
 export function maybeCreateSisyphusConfig(input: {
   disabledAgents: string[]
@@ -84,10 +84,11 @@ export function maybeCreateSisyphusConfig(input: {
   sisyphusConfig = applyOverrides(sisyphusConfig, sisyphusOverride, mergedCategories, directory)
 
   const resolvedModel = sisyphusConfig.model ?? ""
-  const frontierDeny = getFrontierToolSchemaPermission(resolvedModel)
-  if (Object.keys(frontierDeny).length > 0 && sisyphusConfig.permission) {
-    Object.assign(sisyphusConfig.permission, frontierDeny)
-  }
+  sisyphusConfig.permission = applyFrontierToolSchemaPermission(
+    sisyphusConfig.permission,
+    resolvedModel,
+    sisyphusOverride?.permission
+  )
 
   const gptDeny = getGptApplyPatchPermission(resolvedModel)
   if (Object.keys(gptDeny).length > 0 && sisyphusConfig.permission) {