Follow up "Fix shallow clones when upstream attribute is present"

This reverts commit 38d2fe11b9.

Reason for revert: The issue described in I00acd4c61 remains unresolved.
The previous fix incorrectly accessed use_superproject from the Project
class, though it was only defined in ManifestProject. This change uses
it from the manifest attr available in the Project class.

Bug: b/427093249
Change-Id: Ife6d46cd85840f2989f60c2ca4d5a7dcf5d7477a

project.py

@@ -2411,7 +2411,9 @@ class Project:
             # throws an error.
             revs = [f"{self.revisionExpr}^0"]
             upstream_rev = None
-            if self.upstream:
+
+            # Only check upstream when using superproject.
+            if self.upstream and self.manifest.manifestProject.use_superproject:
                 upstream_rev = self.GetRemote().ToLocal(self.upstream)
                 revs.append(upstream_rev)
 
@@ -2423,7 +2425,9 @@ class Project:
                 log_as_error=False,
             )
 
-            if self.upstream:
+            # Only verify upstream relationship for superproject scenarios
+            # without affecting plain usage.
+            if self.upstream and self.manifest.manifestProject.use_superproject:
                 self.bare_git.merge_base(
                     "--is-ancestor",
                     self.revisionExpr,