diff --git a/package-lock.json b/package-lock.json
index bb2b094..3de69ee 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4058,7 +4058,6 @@
       "integrity": "sha512-ekilCSN1jwRvIbgeg/57YFh8qQDNbwDb9xT/qu2DAHbFFZUicIl4ygVaAvzveMhMVr3LnpSKTNnwt8PoOfmKhQ==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "bin": {
         "jiti": "lib/jiti-cli.mjs"
       }
diff --git a/src/repos/config.ts b/src/repos/config.ts
index 978bc8e..f65fc0f 100644
--- a/src/repos/config.ts
+++ b/src/repos/config.ts
@@ -53,8 +53,8 @@ const BASE_REPOS: Omit<RepoConfig, "tag">[] = [
           "docs/developer_versioned_docs/version-{version}",
           "docs/static/aztec-nr-api/devnet",
           "docs/static/typescript-api/devnet",
-          "docs/docs-developers/docs/aztec-nr/debugging.md",
-          "docs/docs-operate/operators/operator-faq.md",
+          "docs/docs-developers/docs/aztec-nr",
+          "docs/docs-operate/operators",
         ],
         branch: "next",
       },
diff --git a/src/utils/git.ts b/src/utils/git.ts
index 556db68..40244fe 100644
--- a/src/utils/git.ts
+++ b/src/utils/git.ts
@@ -101,7 +101,7 @@ export async function cloneRepo(
         const repoGit = simpleGit({ baseDir: clonePath, progress: progressHandler });
         await repoGit.raw(["config", "gc.auto", "0"]);
         log?.(`${config.name}: Setting sparse checkout paths: ${config.sparse!.join(", ")}`, "debug");
-        await repoGit.raw(["sparse-checkout", "set", ...config.sparse!]);
+        await repoGit.raw(["sparse-checkout", "set", "--skip-checks", ...config.sparse!]);
         log?.(`${config.name}: Fetching commit ${config.commit.substring(0, 7)}`, "info");
         await repoGit.fetch(["origin", config.commit]);
         log?.(`${config.name}: Checking out commit`, "debug");
@@ -116,7 +116,7 @@ export async function cloneRepo(
         const repoGit = simpleGit({ baseDir: clonePath, progress: progressHandler });
         await repoGit.raw(["config", "gc.auto", "0"]);
         log?.(`${config.name}: Setting sparse checkout paths: ${config.sparse!.join(", ")}`, "debug");
-        await repoGit.raw(["sparse-checkout", "set", ...config.sparse!]);
+        await repoGit.raw(["sparse-checkout", "set", "--skip-checks", ...config.sparse!]);
         log?.(`${config.name}: Fetching tag ${config.tag}`, "info");
         await repoGit.fetch(["--depth=1", "origin", `refs/tags/${config.tag}:refs/tags/${config.tag}`]);
         log?.(`${config.name}: Checking out tag`, "debug");
@@ -132,7 +132,7 @@ export async function cloneRepo(
         const repoGit = simpleGit({ baseDir: clonePath, progress: progressHandler });
         await repoGit.raw(["config", "gc.auto", "0"]);
         log?.(`${config.name}: Setting sparse checkout paths: ${config.sparse!.join(", ")}`, "debug");
-        await repoGit.raw(["sparse-checkout", "set", ...config.sparse!]);
+        await repoGit.raw(["sparse-checkout", "set", "--skip-checks", ...config.sparse!]);
       }
     } else {
       // Clone for smaller repos
diff --git a/tests/repos/config.test.ts b/tests/repos/config.test.ts
index bf0f12b..0d26ab1 100644
--- a/tests/repos/config.test.ts
+++ b/tests/repos/config.test.ts
@@ -35,8 +35,8 @@ describe("AZTEC_REPOS", () => {
           `docs/developer_versioned_docs/version-${DEFAULT_AZTEC_VERSION}`,
           "docs/static/aztec-nr-api/devnet",
           "docs/static/typescript-api/devnet",
-          "docs/docs-developers/docs/aztec-nr/debugging.md",
-          "docs/docs-operate/operators/operator-faq.md",
+          "docs/docs-developers/docs/aztec-nr",
+          "docs/docs-operate/operators",
         ],
         branch: "next",
       },
diff --git a/tests/utils/git.test.ts b/tests/utils/git.test.ts
index 6781651..0047acb 100644
--- a/tests/utils/git.test.ts
+++ b/tests/utils/git.test.ts
@@ -138,6 +138,7 @@ describe("cloneRepo", () => {
     expect(mockGitInstance.raw).toHaveBeenCalledWith([
       "sparse-checkout",
       "set",
+      "--skip-checks",
       "docs",
       "noir-projects",
     ]);