Update README.md
Fix inconsistencies in README.md files

The two copies of README.MD were inconsistent. This commit corrects this
issue and adds some information about build-time parameters. README.md
remains incomplete, but I'll move the files in "serial" back out. If a
parallel version does happen in the future, I'll handle it
appropriately.
Move files back to the repository root directory

As mentioned in the previous commit message, the "serial" directory is
unnecessary. This commit moves all the files back to the root directory
of the repository.