I encounter a NullPointerException in IndexOrUniqueKeySecondPass with
Hibernate 5.2.10.Final (stack attached).

It appears that problem seems to be linked to
@org.hibernate.annotations.Index (deprecated annotation) used in an
embeddable component, due to the following code that does not consider
that Index can be declared in an embedded field
(IndexOrUniqueKeySecondPass, l.75-76):

PersistentClass persistentClass = (PersistentClass)
persistentClasses.get( column.getPropertyHolder().getEntityName() );
Property property = persistentClass.getProperty( column.getPropertyName() );

This used to work in previous Hibernate version (last known working
version: 5.1.2.Final)

On my side, replacing getPropertyHolder().getEntityName() by
column.getPropertyHolder().getEntityOwnerClassName() fix my problem.

PersistentClass persistentClass = (PersistentClass)
persistentClasses.get(
column.getPropertyHolder().getEntityOwnerClassName() );
Property property = persistentClass.getProperty( column.getPropertyName() );

Encountered stack trace attached to this ticket.
I'm working on a PR.