fix(#2754): include native PluginInput skills in skill() discovery

The skill tool previously only merged disk-discovered skills and preloaded
options.skills, so skills registered natively via ctx.skills (for example
from config.skills.paths or other plugins) were prompt-visible but not
discoverable by skill().

Fix:
- pass ctx.skills from tool-registry into createSkillTool
- extend SkillLoadOptions with nativeSkills accessor
- merge nativeSkills.all() results into getSkills()
- add test covering native PluginInput skill discovery

src/plugin/tool-registry.ts

@@ -1,4 +1,5 @@
 import type { ToolDefinition } from "@opencode-ai/plugin"
+import type { SkillLoadOptions } from "../tools/skill/types"
 
 import type {
   AvailableCategory,
@@ -112,6 +113,7 @@ export function createToolRegistry(args: {
     mcpManager: managers.skillMcpManager,
     getSessionID: getSessionIDForMcp,
     gitMasterConfig: pluginConfig.git_master,
+    nativeSkills: "skills" in ctx ? (ctx as { skills: SkillLoadOptions["nativeSkills"] }).skills : undefined,
   })
 
   // task_system defaults to true since v3.14 — delegation (oracle, subagents) requires it

src/tools/skill/tools.test.ts

@@ -581,3 +581,32 @@ describe("skill tool - dynamic description cache invalidation", () => {
   })
 })
 
+
+
+describe("skill tool - nativeSkills integration", () => {
+  it("merges native skills exposed by PluginInput.skills.all()", async () => {
+    //#given
+    const tool = createSkillTool({
+      skills: [],
+      nativeSkills: {
+        async all() {
+          return [{
+            name: "external-plugin-skill",
+            description: "Skill from config.skills.paths",
+            location: "/external/skills/external-plugin-skill/SKILL.md",
+            content: "External plugin skill body",
+          }]
+        },
+        async get() { return undefined },
+        async dirs() { return [] },
+      },
+    })
+
+    //#when
+    const result = await tool.execute({ name: "external-plugin-skill" }, mockContext)
+
+    //#then
+    expect(result).toContain("external-plugin-skill")
+    expect(result).toContain("Test skill body content")
+  })
+})

src/tools/skill/tools.ts

@@ -190,10 +190,33 @@ export function createSkillTool(options: SkillLoadOptions = {}): ToolDefinition
   const getSkills = async (): Promise<LoadedSkill[]> => {
     clearSkillCache()
     const discovered = await getAllSkills({disabledSkills: options?.disabledSkills})
-    if (!options.skills) return discovered
-    const discoveredNames = new Set(discovered.map(s => s.name))
-    const extras = options.skills.filter(s => !discoveredNames.has(s.name))
-    return [...discovered, ...extras]
+    const allSkills = !options.skills
+      ? discovered
+      : [...discovered, ...options.skills.filter(s => !new Set(discovered.map(d => d.name)).has(s.name))]
+
+    if (options.nativeSkills) {
+      const knownNames = new Set(allSkills.map(s => s.name))
+      try {
+        const nativeAll = await options.nativeSkills.all()
+        for (const native of nativeAll) {
+          if (knownNames.has(native.name)) continue
+          allSkills.push({
+            name: native.name,
+            path: native.location,
+            definition: {
+              name: native.name,
+              description: native.description,
+              template: native.content,
+            },
+            scope: "config",
+          })
+        }
+      } catch {
+        // Native skill discovery may not be available
+      }
+    }
+
+    return allSkills
   }
 
   const getCommands = (): CommandInfo[] => {

src/tools/skill/types.ts

@@ -37,4 +37,10 @@ export interface SkillLoadOptions {
   pluginsEnabled?: boolean
   /** Override plugin enablement from Claude settings by plugin key */
   enabledPluginsOverride?: Record<string, boolean>
+  /** Native skill accessor from PluginInput for discovering skills registered via config.skills.paths */
+  nativeSkills?: {
+    all(): Promise<{ name: string; description: string; location: string; content: string }[]>
+    get(name: string): Promise<{ name: string; description: string; location: string; content: string } | undefined>
+    dirs(): Promise<string[]>
+  }
 }