diff --git a/bin/oh-my-opencode.js b/bin/oh-my-opencode.js
old mode 100644
new mode 100755
diff --git a/src/agents/utils.test.ts b/src/agents/utils.test.ts
index 98c740c35..689e4d314 100644
--- a/src/agents/utils.test.ts
+++ b/src/agents/utils.test.ts
@@ -740,6 +740,52 @@ describe("override.category expansion in createBuiltinAgents", () => {
   })
 })
 
+describe("agent override tools migration", () => {
+  test("tools: { x: false } is migrated to permission: { x: deny }", async () => {
+    // #given
+    const overrides = {
+      explore: { tools: { "jetbrains_*": false } } as any,
+    }
+
+    // #when
+    const agents = await createBuiltinAgents([], overrides, undefined, TEST_DEFAULT_MODEL)
+
+    // #then
+    expect(agents.explore).toBeDefined()
+    const permission = agents.explore.permission as Record<string, string>
+    expect(permission["jetbrains_*"]).toBe("deny")
+  })
+
+  test("tools: { x: true } is migrated to permission: { x: allow }", async () => {
+    // #given
+    const overrides = {
+      librarian: { tools: { "jetbrains_get_*": true } } as any,
+    }
+
+    // #when
+    const agents = await createBuiltinAgents([], overrides, undefined, TEST_DEFAULT_MODEL)
+
+    // #then
+    expect(agents.librarian).toBeDefined()
+    const permission = agents.librarian.permission as Record<string, string>
+    expect(permission["jetbrains_get_*"]).toBe("allow")
+  })
+
+  test("tools config is removed after migration", async () => {
+    // #given
+    const overrides = {
+      explore: { tools: { "some_tool": false } } as any,
+    }
+
+    // #when
+    const agents = await createBuiltinAgents([], overrides, undefined, TEST_DEFAULT_MODEL)
+
+    // #then
+    expect(agents.explore).toBeDefined()
+    expect((agents.explore as any).tools).toBeUndefined()
+  })
+})
+
 describe("Deadlock prevention - fetchAvailableModels must not receive client", () => {
    test("createBuiltinAgents should call fetchAvailableModels with undefined client to prevent deadlock", async () => {
      // #given - This test ensures we don't regress on issue #1301
diff --git a/src/agents/utils.ts b/src/agents/utils.ts
index 7c1a236d5..426a8bd08 100644
--- a/src/agents/utils.ts
+++ b/src/agents/utils.ts
@@ -11,7 +11,7 @@ import { createAtlasAgent, atlasPromptMetadata } from "./atlas"
 import { createMomusAgent, momusPromptMetadata } from "./momus"
 import { createHephaestusAgent } from "./hephaestus"
 import type { AvailableAgent, AvailableCategory, AvailableSkill } from "./dynamic-agent-prompt-builder"
-import { deepMerge, fetchAvailableModels, resolveModelPipeline, AGENT_MODEL_REQUIREMENTS, readConnectedProvidersCache, isModelAvailable, isAnyFallbackModelAvailable } from "../shared"
+import { deepMerge, fetchAvailableModels, resolveModelPipeline, AGENT_MODEL_REQUIREMENTS, readConnectedProvidersCache, isModelAvailable, isAnyFallbackModelAvailable, migrateAgentConfig } from "../shared"
 import { DEFAULT_CATEGORIES, CATEGORY_DESCRIPTIONS } from "../tools/delegate-task/constants"
 import { resolveMultipleSkills } from "../features/opencode-skill-loader/skill-content"
 import { createBuiltinSkills } from "../features/builtin-skills"
@@ -207,7 +207,8 @@ function mergeAgentConfig(
   base: AgentConfig,
   override: AgentOverrideConfig
 ): AgentConfig {
-  const { prompt_append, ...rest } = override
+  const migratedOverride = migrateAgentConfig(override as Record<string, unknown>) as AgentOverrideConfig
+  const { prompt_append, ...rest } = migratedOverride
   const merged = deepMerge(base, rest as Partial<AgentConfig>)
 
   if (prompt_append && merged.prompt) {