fix: wire host config.skills.paths into agent skill discovery

When another plugin (e.g. superpowers) injects skill directories via config.skills.paths in the config hook, the agent-config-handler now discovers those skills via a second discoverConfigSourceSkills call using the adapted host config. Fixes #3396.

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

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

src/plugin-handlers/agent-config-handler-agents-skills.test.ts

@@ -122,4 +122,50 @@ describe("applyAgentConfig .agents skills", () => {
     expect(discoveredSkills.map(skill => skill.name)).toContain("project-agent-skill")
     expect(discoveredSkills.map(skill => skill.name)).toContain("global-agent-skill")
   })
+
+  test("discovers skills from host config.skills.paths set by other plugins", async () => {
+    // given - second call to discoverConfigSourceSkills returns host config skills
+    discoverConfigSourceSkillsSpy
+      .mockResolvedValueOnce([])
+      .mockResolvedValueOnce([
+        {
+          name: "host-config-skill",
+          definition: { name: "host-config-skill", template: "host-template" },
+          scope: "config",
+        },
+      ])
+
+    // when
+    await applyAgentConfig({
+      config: {
+        model: "anthropic/claude-opus-4-6",
+        agent: {},
+        skills: { paths: ["/host/skills"] },
+      },
+      pluginConfig: createPluginConfig(),
+      ctx: { directory: "/tmp/project" },
+      pluginComponents: createPluginComponents(),
+    })
+
+    // then
+    const discoveredSkills = createBuiltinAgentsSpy.mock.calls[0]?.[6] as Array<{ name: string }>
+    expect(discoveredSkills.map(skill => skill.name)).toContain("host-config-skill")
+  })
+
+  test("calls discoverConfigSourceSkills twice when host config has skills", async () => {
+    // when
+    await applyAgentConfig({
+      config: {
+        model: "anthropic/claude-opus-4-6",
+        agent: {},
+        skills: { paths: ["/host/skills"] },
+      },
+      pluginConfig: createPluginConfig(),
+      ctx: { directory: "/tmp/project" },
+      pluginComponents: createPluginComponents(),
+    })
+
+    // then - called twice: once for pluginConfig.skills, once for host config.skills
+    expect(discoverConfigSourceSkillsSpy).toHaveBeenCalledTimes(2)
+  })
 })

src/plugin-handlers/agent-config-handler.ts

@@ -35,6 +35,7 @@ import {
 } from "./agent-override-protection";
 import { buildPrometheusAgentConfig } from "./prometheus-agent-config-builder";
 import { buildPlanDemoteConfig } from "./plan-model-inheritance";
+import { adaptHostSkillConfig } from "../shared/host-skill-config";
 
 type AgentConfigRecord = Record<string, Record<string, unknown> | undefined> & {
   build?: Record<string, unknown>;
@@ -61,8 +62,10 @@ export async function applyAgentConfig(params: {
   ) as typeof params.pluginConfig.disabled_agents;
 
   const includeClaudeSkillsForAwareness = params.pluginConfig.claude_code?.skills ?? true;
+  const hostSkillConfig = adaptHostSkillConfig(params.config.skills);
   const [
     discoveredConfigSourceSkills,
+    discoveredHostConfigSkills,
     discoveredUserSkills,
     discoveredProjectSkills,
     discoveredProjectAgentsSkills,
@@ -74,6 +77,10 @@ export async function applyAgentConfig(params: {
       config: params.pluginConfig.skills,
       configDir: params.ctx.directory,
     }),
+    discoverConfigSourceSkills({
+      config: hostSkillConfig,
+      configDir: params.ctx.directory,
+    }),
     includeClaudeSkillsForAwareness ? discoverUserClaudeSkills() : Promise.resolve([]),
     includeClaudeSkillsForAwareness
        ? discoverProjectClaudeSkills(params.ctx.directory)
@@ -88,6 +95,7 @@ export async function applyAgentConfig(params: {
 
   const allDiscoveredSkills = [
     ...discoveredConfigSourceSkills,
+    ...discoveredHostConfigSkills,
     ...discoveredOpencodeProjectSkills,
     ...discoveredProjectSkills,
     ...discoveredProjectAgentsSkills,