diff --git a/lib/analyse.ml b/lib/analyse.ml
index 7eaa9b56..791fc1a3 100644
--- a/lib/analyse.ml
+++ b/lib/analyse.ml
@@ -195,8 +195,6 @@ module Analysis = struct
         | Error _ as err -> Lwt.return err
         | Ok pkgs ->
           match String.split_on_char '/' path with
-          | [_] | ".github"::_ ->
-            Lwt_result.return pkgs
           | "packages" :: name :: package :: "files" :: _ ->
             Lwt_result.return (add_pkg ~path ~name ~package SignificantlyChanged pkgs)
           | ["packages"; name; package; "opam"] ->
@@ -211,8 +209,11 @@ module Analysis = struct
                 get_opam ~cwd:dir path
                 >>= add_changed_pkg ~path ~name ~package ~old_content pkgs
             end
+          | "packages" :: _ ->
+            Fmt.failwith "Unexpected path %S in packages directory (expecting 'packages/name/name.l.m.n/{opam,files/*}')" path
           | _ ->
-            Fmt.failwith "Unexpected path %S in output (expecting 'packages/name/pkg/...')" path
+            (* Changes to any other path should be reviewed manually, since it's a change into repository meta data *)
+            Lwt_result.return pkgs
       ) (Ok OpamPackage.Map.empty)
 
   let has_tests opam =
diff --git a/test/analyse.t b/test/analyse.t
index cd8d12a0..4872b8da 100644
--- a/test/analyse.t
+++ b/test/analyse.t
@@ -111,6 +111,15 @@ See https://github.com/ocurrent/opam-repo-ci/issues/291
   $ opam-repo-ci-local --repo="." --branch=analyze-invalid-opam-file --analyse-only --no-web-server
   Error ""packages/a-1/a-1.0.0.1/opam" failed to be parsed: '.' is not a valid token"
 
-Clean up the build cache
+  $ rm -rf var
 
-  $ rm -rf ./var
+Test that a new root directory can be created.
+See https://github.com/ocurrent/opam-repo-ci/pull/397
+
+  $ git checkout -q -b add-a-new-dir initial-state
+  $ mkdir a-new-directory
+  $ touch a-new-directory/foo
+  $ git add  a-new-directory/foo
+  $ git commit -q -m "Add a new directory"
+  $ opam-repo-ci-local --repo="." --branch=add-a-new-dir --analyse-only --no-web-server
+  { "packages": [] }