Tweaks to Makefile and gitignore

Previous Makefile was fine, but I've added some comments
on the more general techniques that make it easier to
scale up to larger builds.
minor tweaks to top-level make
moved over tweaks from top-level main. Works for me, but should probably be using an installed version of the lib
ignoring build products
pulling out the newick parsing
environment file
assembla PLL environment
modifying varnames for assembla version of repo
removed redundancy
actually reads newick!
checks validity of newick
building
pll instance
Merge branch 'assembla'
closer