Add 0x800 (supplementary alignment) flag.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1564 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a method to take in a list of files which are a mix of "usable" files and text files listing one usable file per line and process it into a larger list of usable files.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1565 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'