1.)    After I have done an initial  "./build.sh package",  where do I make 
changes to files in the target directory that will not disappear on my next 
"package" but rather are in corporated into the .WAR file --style changes as 
well as configuration changes.



Depends on what sort of changes. Typically it’s either etc/cas/config or 
src/main/resources.


2.) I am under the impression that SAML support is much move developed in 
version 5 than 4  -- is this assumption correct?



Yes..



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