diff --git a/lib/kit.mjs b/lib/kit.mjs
index 1983215..b85ad5e 100644
--- a/lib/kit.mjs
+++ b/lib/kit.mjs
@@ -146,37 +146,40 @@ export function mergePackageScripts(targetRoot, repoName) {
 export function appendGitignore(targetRoot, runtime = "both") {
   const gi = path.join(targetRoot, ".gitignore");
   const existing = fs.existsSync(gi) ? fs.readFileSync(gi, "utf8") : "";
-  if (existing.includes(GITIGNORE_MARKER)) return [];
-  const snippet = buildGitignoreSnippet(parseRuntime(runtime));
-  fs.appendFileSync(gi, snippet);
-  return snippet.trim().split("\n").filter(Boolean);
+  const block = buildGitignoreSnippet(parseRuntime(runtime)).trim();
+  // Refresh the managed block on every install/update so upgrades pick up ignore
+  // rules added in newer versions (e.g. .agents/skills, .gitnexus/, the tracked
+  // store) instead of leaving an older install's stale block untouched.
+  const base = stripManagedGitignoreBlock(existing).replace(/\n+$/, "");
+  const next = base ? `${base}\n\n${block}\n` : `${block}\n`;
+  fs.writeFileSync(gi, next);
+  return block.split("\n").filter((l) => l && !l.startsWith("#"));
+}
+
+/**
+ * Remove the managed block (marker comment + its contiguous non-blank lines),
+ * absorbing one surrounding blank line so we don't leave doubled blanks.
+ * @param {string} text @returns {string}
+ */
+function stripManagedGitignoreBlock(text) {
+  if (!text.includes(GITIGNORE_MARKER)) return text;
+  const lines = text.split("\n");
+  let start = lines.findIndex((l) => l.includes(GITIGNORE_MARKER));
+  if (start === -1) return text;
+  let end = start;
+  while (end < lines.length && lines[end].trim() !== "") end++;
+  if (start > 0 && lines[start - 1].trim() === "") start--;
+  if (end < lines.length && lines[end].trim() === "") end++;
+  lines.splice(start, end - start);
+  return lines.join("\n");
 }
 
 /** @param {string} targetRoot */
 export function removeGitignoreSnippet(targetRoot) {
   const gi = path.join(targetRoot, ".gitignore");
   if (!fs.existsSync(gi)) return;
-  const lines = fs.readFileSync(gi, "utf8").split("\n");
-  const out = [];
-  let skipping = false;
-  for (const line of lines) {
-    if (line.includes(GITIGNORE_MARKER)) {
-      skipping = true;
-      continue;
-    }
-    if (skipping) {
-      if (
-        line.trim() === "" &&
-        out.length > 0 &&
-        out[out.length - 1]?.trim() === ""
-      ) {
-        skipping = false;
-      }
-      continue;
-    }
-    out.push(line);
-  }
-  fs.writeFileSync(gi, out.join("\n").replace(/\n+$/, "\n"));
+  const stripped = stripManagedGitignoreBlock(fs.readFileSync(gi, "utf8"));
+  fs.writeFileSync(gi, stripped.replace(/\n+$/, "\n"));
 }
 
 /** @param {string} targetRoot @param {string[]} [keys] Keys to remove (defaults to all managed). */
diff --git a/lib/kit.test.mjs b/lib/kit.test.mjs
index 41b775f..ab1ae1c 100644
--- a/lib/kit.test.mjs
+++ b/lib/kit.test.mjs
@@ -650,6 +650,30 @@ describe("gitnexus-agent-kit", () => {
     assert.ok(GITIGNORE_MARKER.includes("GitNexus + gitnexus-agent-kit"));
   });
 
+  it("appendGitignore refreshes an existing managed block on upgrade", async () => {
+    const { appendGitignore } = await import("./kit.mjs");
+    const tmp = fs.mkdtempSync(path.join(os.tmpdir(), "gn-gi-refresh-"));
+    // An older install: managed block predates .agents/skills and .gitnexus/.
+    fs.writeFileSync(
+      path.join(tmp, ".gitignore"),
+      `node_modules/\n\n${GITIGNORE_MARKER} (safe to remove)\n.tmp-agent/\n.cursor/skills/\n`,
+    );
+    appendGitignore(tmp, "all");
+    const gi = fs.readFileSync(path.join(tmp, ".gitignore"), "utf8");
+    // Block refreshed to the current scheme: graph index + all IDE skill dirs ignored.
+    assert.ok(gi.includes(".gitnexus/"), "adds .gitnexus/ ignore on upgrade");
+    assert.ok(gi.includes(".agents/skills/"), "adds .agents/skills on upgrade");
+    assert.ok(gi.includes(".claude/skills/"), "adds .claude/skills on upgrade");
+    // User content preserved; marker not duplicated.
+    assert.ok(gi.includes("node_modules/"));
+    assert.equal(gi.split(GITIGNORE_MARKER).length - 1, 1);
+    // Idempotent: a second pass keeps a single block.
+    appendGitignore(tmp, "all");
+    const gi2 = fs.readFileSync(path.join(tmp, ".gitignore"), "utf8");
+    assert.equal(gi2.split(GITIGNORE_MARKER).length - 1, 1);
+    fs.rmSync(tmp, { recursive: true, force: true });
+  });
+
   it("enforcement rule includes graph+embeddings gates", () => {
     const rule = fs.readFileSync(
       path.join(BUNDLE_ROOT, ".cursor/rules/00-gitnexus-enforcement.mdc"),