Pass secondary alignments through unchanged.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1352 8bce386e-0d6e-43e0-b1ca-608082c0432d
Updating documentation

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1353 8bce386e-0d6e-43e0-b1ca-608082c0432d
Updating documentation

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1354 8bce386e-0d6e-43e0-b1ca-608082c0432d
Updating documentation

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1355 8bce386e-0d6e-43e0-b1ca-608082c0432d
Updating documentation

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1356 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a constructor to Allele that takes in an Allele as input and makes a copy without having to go through the validation of the bases (since the original Allele has already been validated).

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1357 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge branch 'svntrack'
build partial javadocs to tmpdir (to avoid unnecessary rebuild), stage maven artifacts to subdir
Merge branch 'master' into maven-repo