diff --git a/packages/cli/src/utils/skillsManifest.test.ts b/packages/cli/src/utils/skillsManifest.test.ts
index 71e4cea5c4f..0ec1c11f2df 100644
--- a/packages/cli/src/utils/skillsManifest.test.ts
+++ b/packages/cli/src/utils/skillsManifest.test.ts
@@ -90,6 +90,33 @@ describe("hashSkillBundle", () => {
     expect(hashSkillBundle(dir).files).toBe(3);
   });
 
+  it("ignores Python bytecode a skill script leaves behind, but not a real edit", () => {
+    const dir = writeSkill("a", {
+      "SKILL.md": "hello",
+      "scripts/lib/auth.py": "x = 1\n",
+    });
+    const clean = hashSkillBundle(dir);
+    mkdirSync(join(dir, "scripts/lib/__pycache__"));
+    writeFileSync(join(dir, "scripts/lib/__pycache__/auth.cpython-312.pyc"), "\x00bytecode");
+    writeFileSync(join(dir, "scripts/lib/stray.pyc"), "\x00bytecode");
+    expect(hashSkillBundle(dir)).toEqual(clean);
+
+    writeFileSync(join(dir, "scripts/lib/auth.py"), "x = 2\n");
+    expect(hashSkillBundle(dir).hash).not.toBe(clean.hash);
+  });
+
+  it("ignores dependency installs, OS files, and editor swap files", () => {
+    const dir = writeSkill("a", { "SKILL.md": "hello", "scripts/run.mjs": "run();" });
+    const clean = hashSkillBundle(dir);
+    writeSkill("a", {
+      "node_modules/dep/index.js": "module.exports = 1;",
+      "scripts/.DS_Store": "",
+      "scripts/.run.mjs.swp": "swap",
+      "SKILL.md~": "backup",
+    });
+    expect(hashSkillBundle(dir)).toEqual(clean);
+  });
+
   it("normalises CRLF so a Windows checkout is not flagged as different", () => {
     const lf = writeSkill("lf", { "SKILL.md": "line1\nline2\n" });
     const crlf = writeSkill("crlf", { "SKILL.md": "line1\r\nline2\r\n" });
diff --git a/packages/cli/src/utils/skillsManifest.ts b/packages/cli/src/utils/skillsManifest.ts
index 77b2dbfb7dd..80949bdb498 100644
--- a/packages/cli/src/utils/skillsManifest.ts
+++ b/packages/cli/src/utils/skillsManifest.ts
@@ -162,14 +162,33 @@ export const FALLBACK_CORE_SKILLS: readonly string[] = [
 
 // ── Hashing ────────────────────────────────────────────────────────────────
 
+// By-products of using a skill (bytecode from running its scripts, installs, OS
+// and editor files), skipped on both the source and the installed side so a
+// tree that ran a script hashes the same as a clean checkout.
+const RUNTIME_DIRS = new Set([
+  "__pycache__",
+  ".pytest_cache",
+  ".mypy_cache",
+  ".ruff_cache",
+  "node_modules",
+]);
+const RUNTIME_FILES = new Set([".DS_Store", "Thumbs.db"]);
+const RUNTIME_FILE_SUFFIXES = [".pyc", ".pyo", ".swp", ".swo", "~"];
+
+function isRuntimeFile(name: string): boolean {
+  return RUNTIME_FILES.has(name) || RUNTIME_FILE_SUFFIXES.some((s) => name.endsWith(s));
+}
+
 function listFilesSorted(dir: string): string[] {
   const out: string[] = [];
   const walk = (d: string): void => {
     for (const name of readdirSync(d)) {
-      if (name === ".DS_Store") continue;
       const p = join(d, name);
-      if (statSync(p).isDirectory()) walk(p);
-      else out.push(p);
+      if (statSync(p).isDirectory()) {
+        if (!RUNTIME_DIRS.has(name)) walk(p);
+      } else if (!isRuntimeFile(name)) {
+        out.push(p);
+      }
     }
   };
   walk(dir);