fix(skill): isolate injected skill discovery

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

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

src/tools/skill/tools.factory.test.ts

@@ -4,13 +4,10 @@ import { afterEach, beforeEach, describe, expect, it, mock, spyOn } from "bun:te
 import type { ToolContext } from "@opencode-ai/plugin/tool"
 import type { LoadedSkill } from "../../features/opencode-skill-loader/types"
 import * as skillContent from "../../features/opencode-skill-loader/skill-content"
+import * as commandDiscovery from "../slashcommand/command-discovery"
 
 const discoverCommandsSync = mock(() => [])
 
-mock.module("../slashcommand/command-discovery", () => ({
-  discoverCommandsSync,
-}))
-
 function createMockSkill(name: string): LoadedSkill {
   return {
     name,
@@ -50,6 +47,7 @@ function createMockContext(sessionID: string): ToolContext {
 }
 
 beforeEach(() => {
+  spyOn(commandDiscovery, "discoverCommandsSync").mockImplementation(discoverCommandsSync)
   spyOn(skillContent, "getAllSkills").mockImplementation(getAllSkills)
   spyOn(skillContent, "clearSkillCache").mockImplementation(clearSkillCache)
 })

src/tools/skill/tools.ts

@@ -37,14 +37,7 @@ export function createSkillTool(options: SkillLoadOptions = {}): ToolDefinition
       disabledSkills: options?.disabledSkills,
       browserProvider: options?.browserProvider,
     })) ?? []
-    const allSkills = !options.skills
-      ? discovered
-      : [
-          ...discovered,
-          ...options.skills.filter(
-            (skill) => !new Set(discovered.map((discoveredSkill) => discoveredSkill.name)).has(skill.name)
-          ),
-        ]
+    const allSkills = options.skills ? [...options.skills] : discovered
 
     if (options.nativeSkills) {
       try {