diff --git a/packages/opencode/src/skill/skill.ts b/packages/opencode/src/skill/skill.ts
index fa984b3e111..f52723a3a7f 100644
--- a/packages/opencode/src/skill/skill.ts
+++ b/packages/opencode/src/skill/skill.ts
@@ -54,9 +54,11 @@ export namespace Skill {
 
   export const state = Instance.state(async () => {
     const skills: Record<string, Info> = {}
-    const dirs = new Set<string>()
+    const dirs = new Map<string, string>()
+    const seen = new Map<string, string>()
 
     const addSkill = async (match: string) => {
+      const real = Filesystem.resolve(match)
       const md = await ConfigMarkdown.parse(match).catch((err) => {
         const message = ConfigMarkdown.FrontmatterError.isInstance(err)
           ? err.data.message
@@ -71,16 +73,23 @@ export namespace Skill {
       const parsed = Info.pick({ name: true, description: true }).safeParse(md.data)
       if (!parsed.success) return
 
-      // Warn on duplicate skill names
-      if (skills[parsed.data.name]) {
+      const prev = skills[parsed.data.name]
+      if (prev && Filesystem.resolve(prev.location) !== real) {
         log.warn("duplicate skill name", {
           name: parsed.data.name,
-          existing: skills[parsed.data.name].location,
+          existing: prev.location,
           duplicate: match,
         })
       }
 
-      dirs.add(path.dirname(match))
+      const old = seen.get(real)
+      if (old && old !== parsed.data.name) {
+        const skill = skills[old]
+        if (skill && Filesystem.resolve(skill.location) === real) delete skills[old]
+      }
+
+      dirs.set(path.dirname(real), path.dirname(match))
+      seen.set(real, parsed.data.name)
 
       skills[parsed.data.name] = {
         name: parsed.data.name,
@@ -159,7 +168,6 @@ export namespace Skill {
     for (const url of config.skills?.urls ?? []) {
       const list = await Discovery.pull(url)
       for (const dir of list) {
-        dirs.add(dir)
         const matches = await Glob.scan(SKILL_PATTERN, {
           cwd: dir,
           absolute: true,
@@ -174,7 +182,7 @@ export namespace Skill {
 
     return {
       skills,
-      dirs: Array.from(dirs),
+      dirs: Array.from(dirs.values()),
     }
   })
 
diff --git a/packages/opencode/test/agent/agent.test.ts b/packages/opencode/test/agent/agent.test.ts
index 497b6019d3e..acaf1bb3f3d 100644
--- a/packages/opencode/test/agent/agent.test.ts
+++ b/packages/opencode/test/agent/agent.test.ts
@@ -1,5 +1,6 @@
 import { test, expect } from "bun:test"
 import path from "path"
+import fs from "fs/promises"
 import { tmpdir } from "../fixture/fixture"
 import { Instance } from "../../src/project/instance"
 import { Agent } from "../../src/agent/agent"
@@ -564,6 +565,45 @@ description: Permission skill.
   }
 })
 
+test("symlinked skill aliases add one external_directory allow rule", async () => {
+  await using tmp = await tmpdir({
+    git: true,
+    init: async (dir) => {
+      const claude = path.join(dir, ".claude", "skills", "shared-skill")
+      const agents = path.join(dir, ".agents", "skills")
+      await Bun.write(
+        path.join(claude, "SKILL.md"),
+        `---
+name: shared-skill
+description: Shared skill.
+---
+
+# Shared Skill
+`,
+      )
+      await fs.mkdir(agents, { recursive: true })
+      await fs.symlink(claude, path.join(agents, "shared-skill"), "dir")
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const build = await Agent.get("build")
+      const rules = build!.permission.filter(
+        (rule) =>
+          rule.permission === "external_directory" &&
+          rule.action === "allow" &&
+          rule.pattern.includes("shared-skill") &&
+          rule.pattern.endsWith("*"),
+      )
+
+      expect(rules).toHaveLength(1)
+      expect(rules[0].pattern).toBe(path.join(tmp.path, ".agents", "skills", "shared-skill", "*"))
+    },
+  })
+})
+
 test("defaultAgent returns build when no default_agent config", async () => {
   await using tmp = await tmpdir()
   await Instance.provide({
diff --git a/packages/opencode/test/skill/skill.test.ts b/packages/opencode/test/skill/skill.test.ts
index 2264723a090..366754c8a48 100644
--- a/packages/opencode/test/skill/skill.test.ts
+++ b/packages/opencode/test/skill/skill.test.ts
@@ -386,3 +386,36 @@ description: A skill in the .opencode/skills directory.
     },
   })
 })
+
+test("dedupes symlinked skill aliases and keeps the later path", async () => {
+  await using tmp = await tmpdir({
+    git: true,
+    init: async (dir) => {
+      const claude = path.join(dir, ".claude", "skills", "shared-skill")
+      const agents = path.join(dir, ".agents", "skills")
+      await Bun.write(
+        path.join(claude, "SKILL.md"),
+        `---
+name: shared-skill
+description: Shared skill.
+---
+
+# Shared Skill
+`,
+      )
+      await fs.mkdir(agents, { recursive: true })
+      await fs.symlink(claude, path.join(agents, "shared-skill"), "dir")
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const skills = await Skill.all()
+      const dirs = await Skill.dirs()
+      expect(skills).toHaveLength(1)
+      expect(skills[0].location).toContain(path.join(".agents", "skills", "shared-skill", "SKILL.md"))
+      expect(dirs).toEqual([path.join(tmp.path, ".agents", "skills", "shared-skill")])
+    },
+  })
+})