prefer long option names in scripts
remove Makefile.local

This is an intermediate step towards vendoring samtools.
remove "dependency file" generation

The way this was done causes "building" to happen even when trying to
make non-build targets, e.g. config and clean.  The "dependency files"
don't appear to be required to successfully build.
add missing file to clean target
vendor samtools
remove phony config target from pindel and pindel-debug targets
add .travis.yml