Filter out GIT_DIR from cloner environment variables (#3760)

Co-authored-by: Edward McFarlane <emcfarlane@buf.build>

Author: doriable

private/pkg/git/cloner.go

@@ -76,6 +76,13 @@ func (c *cloner) CloneToBucket(
 
 	depthArg := strconv.Itoa(int(depth))
 
+	envContainer = app.NewEnvContainerWithOverrides(envContainer, map[string]string{
+		// In the case where this is being run in an environment where GIT_DIR is set, e.g. within
+		// a submodule, we want to treat this as a stand-alone clone rather than interacting with
+		// an existing GIT_DIR. So we filter out GIT_DIR from our environment variables.
+		"GIT_DIR": "",
+	})
+
 	baseDir, err := tmp.NewDir(ctx)
 	if err != nil {
 		return err