The jarsigner tool has a warning "This jar contains signed entries that are not signed by alias in this keystore" which should be shown when a signed entry's signer cert does not appear in this keystore. However, if the 3 following conditions satisfy this warning is NOT shown:

1. signer has a cert chain
2. end-entity cert is NOT in this keystore
3. one of the intermediate CA certs is in this keystore

This is a bug. The warning should only check the end-entity cert.