Cleaned up loci.common.* legacy packages

Cleaned up loci.common, loci.common.adapter, loci.common.enumeration and
loci.common.xml packages. These were done together because changes in
some packages affected other packages as well. All affected classes were
delegators or adapters between legacy and modern classes.

Converted many classes that effectively were Wrappers to implement the
Wrapper interface. Removed unnecessary/dangerous methods, including
Object overrides. Added more javadoc. Added deprecation annotations.