fix(agents): preserve explicit legacy 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

@@ -93,7 +93,8 @@ export function maybeCreateHephaestusConfig(input: {
   hephaestusConfig.permission = applyFrontierToolSchemaPermission(
     hephaestusConfig.permission,
     resolvedModel,
-    hephaestusOverride?.permission
+    hephaestusOverride?.permission,
+    (hephaestusOverride as { tools?: Record<string, boolean> } | undefined)?.tools
   )
 
   const gptDeny = getGptApplyPatchPermission(resolvedModel)

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

@@ -212,6 +212,41 @@ describe("maybeCreateSisyphusConfig", () => {
     });
   });
 
+  describe("#given non-frontier model with legacy user tools denying grep and glob", () => {
+    test("#when config is created #then explicit legacy denies are preserved", () => {
+      // given
+      const legacyOverride = {
+        model: "openai/gpt-5.4",
+        tools: {
+          grep: false,
+          glob: false,
+        },
+      };
+      const agentOverrides: AgentOverrides = {
+        sisyphus: legacyOverride,
+      };
+      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

@@ -87,7 +87,8 @@ export function maybeCreateSisyphusConfig(input: {
   sisyphusConfig.permission = applyFrontierToolSchemaPermission(
     sisyphusConfig.permission,
     resolvedModel,
-    sisyphusOverride?.permission
+    sisyphusOverride?.permission,
+    (sisyphusOverride as { tools?: Record<string, boolean> } | undefined)?.tools
   )
 
   const gptDeny = getGptApplyPatchPermission(resolvedModel)

src/agents/frontier-tool-schema-guard.ts

@@ -19,7 +19,8 @@ export function getFrontierToolSchemaPermission(model: string): Record<string, "
 export function applyFrontierToolSchemaPermission(
   permission: AgentConfig["permission"] | undefined,
   model: string,
-  explicitPermission?: AgentConfig["permission"]
+  explicitPermission?: AgentConfig["permission"],
+  explicitTools?: Record<string, boolean>
 ): AgentConfig["permission"] | undefined {
   if (!permission) return permission
 
@@ -33,6 +34,7 @@ export function applyFrontierToolSchemaPermission(
 
   for (const toolName of FRONTIER_TOOL_SCHEMA_NAMES) {
     if (explicitPermissionMap?.[toolName] === "deny") continue
+    if (explicitTools?.[toolName] === false) continue
     delete nextPermission[toolName]
   }
   return nextPermission as AgentConfig["permission"]

src/agents/hephaestus/agent.test.ts

@@ -553,4 +553,39 @@ describe("maybeCreateHephaestusConfig GPT apply_patch guard", () => {
       expect(config?.permission).toHaveProperty("glob", "deny");
     });
   });
+
+  describe("#given non-frontier model with legacy user tools denying grep and glob", () => {
+    test("#when config is created #then explicit legacy denies are preserved", () => {
+      // given
+      const legacyOverride = {
+        model: "openai/gpt-5.4",
+        tools: {
+          grep: false,
+          glob: false,
+        },
+      };
+      const agentOverrides: AgentOverrides = {
+        hephaestus: legacyOverride,
+      };
+      const mergedCategories: Record<string, CategoryConfig> = {};
+
+      // when
+      const config = maybeCreateHephaestusConfig({
+        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");
+    });
+  });
 });