bugfixes and save file compatibility

I hit upon an idea to re-init all the classes in the game so that even
when new stuff gets added old save files can be made to be compatible
automatically. it actually seems to work.
added cover mechanic
updated README.md
lots of rewriting ugly old rushed code

not really that much in the way of new features.
getting ready for beta 3 release

* added a new secret weapon
* added HP value on enemy HP bar. removed EN bar
* added basic debuff functionality
* added all of Sam's new work
more works towards beta 3

some smaller tweaks and bug fixes
Merge pull request #5 from vaendryl/master

update to beta 3