Flatten directory structure, fix file permissions, remove some product files

* Flattened the directory structure, pushing everything up one level.
* Added execute permissions to the perl script and all the shell scripts
* I deleted a bunch of *.list files in lib/krypto from the repository.  
  They appear to be products of the build, and were showing up as 
  modified when I did "git status" after the build.
* I added a .gitignore.