diff --git a/skills/diagnose-why-work-stopped/SKILL.md b/.agents/skills/diagnose-why-work-stopped/SKILL.md
similarity index 100%
rename from skills/diagnose-why-work-stopped/SKILL.md
rename to .agents/skills/diagnose-why-work-stopped/SKILL.md
diff --git a/skills/paperclip-create-plugin/SKILL.md b/.agents/skills/paperclip-create-plugin/SKILL.md
similarity index 100%
rename from skills/paperclip-create-plugin/SKILL.md
rename to .agents/skills/paperclip-create-plugin/SKILL.md
diff --git a/skills/terminal-bench-loop/SKILL.md b/.agents/skills/terminal-bench-loop/SKILL.md
similarity index 99%
rename from skills/terminal-bench-loop/SKILL.md
rename to .agents/skills/terminal-bench-loop/SKILL.md
index ce2c4f22..6a3c8d21 100644
--- a/skills/terminal-bench-loop/SKILL.md
+++ b/.agents/skills/terminal-bench-loop/SKILL.md
@@ -228,7 +228,7 @@ The command uses the current Paperclip API token and company from `PAPERCLIP_API
 
 The smoke is deterministic and intentionally non-comparable. It does not start Terminal-Bench, Harbor, an agent model, or a provider runtime. It verifies only the control-plane shape:
 
-- local `skills/terminal-bench-loop/SKILL.md` contains the loop contract terms;
+- local `.agents/skills/terminal-bench-loop/SKILL.md` contains the loop contract terms;
 - a top-level loop issue can be created and updated into a blocker posture;
 - an iteration child issue can be created under the loop parent;
 - mocked benchmark artifact paths are recorded on a `run` document;
diff --git a/scripts/smoke/terminal-bench-loop-skill-smoke.mjs b/scripts/smoke/terminal-bench-loop-skill-smoke.mjs
index f8253a59..ddceb3bd 100755
--- a/scripts/smoke/terminal-bench-loop-skill-smoke.mjs
+++ b/scripts/smoke/terminal-bench-loop-skill-smoke.mjs
@@ -83,7 +83,7 @@ function assert(condition, message) {
 }
 
 async function assertLocalSkillPackage() {
-  const skillPath = join(repoRoot, "skills", "terminal-bench-loop", "SKILL.md");
+  const skillPath = join(repoRoot, ".agents", "skills", "terminal-bench-loop", "SKILL.md");
   const markdown = await readFile(skillPath, "utf8");
   for (const expected of [
     "name: terminal-bench-loop",
diff --git a/server/src/__tests__/paperclip-skill-utils.test.ts b/server/src/__tests__/paperclip-skill-utils.test.ts
index aae6c70a..a8415c20 100644
--- a/server/src/__tests__/paperclip-skill-utils.test.ts
+++ b/server/src/__tests__/paperclip-skill-utils.test.ts
@@ -27,7 +27,10 @@ describe("paperclip skill utils", () => {
     await fs.mkdir(moduleDir, { recursive: true });
     await fs.mkdir(path.join(root, "skills", "paperclip"), { recursive: true });
     await fs.mkdir(path.join(root, "skills", "paperclip-create-agent"), { recursive: true });
+    await fs.mkdir(path.join(root, ".agents", "skills", "diagnose-why-work-stopped"), { recursive: true });
+    await fs.mkdir(path.join(root, ".agents", "skills", "paperclip-create-plugin"), { recursive: true });
     await fs.mkdir(path.join(root, ".agents", "skills", "release"), { recursive: true });
+    await fs.mkdir(path.join(root, ".agents", "skills", "terminal-bench-loop"), { recursive: true });
 
     const entries = await listPaperclipSkillEntries(moduleDir);