One corrupt manifest should not wedge model operations (#7515)

One potential failure mode is an empty file which bubbles up as an EOF error,
leading to all pulls and listing operations failing.  Instead, continue and
warn about the corrupt manifest.  This also allows re-pulling the corrupt
manifest to repair the system.

server/manifest_test.go

@@ -112,7 +112,7 @@ func TestManifests(t *testing.T) {
 				createManifest(t, d, p)
 			}
 
-			ms, err := Manifests()
+			ms, err := Manifests(true)
 			if err != nil {
 				t.Fatal(err)
 			}