Rewrite README

There is a lot of changes
Remove uselesss header comments
Rename variable
Reference correct README file
Refactor ls_files and how to get file lists in general

The diff is horrible.
I added the get_..._files functions that will provide the file lists.
And changed the ls_files to be the main body of the ls-files command like
it should be.
Any named pipes or weird cache functions are out of the window!
Add some TODO bits
Change git invocation
Reformat help messages
Add TODO bit
Reword any instance of link, symlink to symbolic link
Revamp README
Revamp help and status texts