Fixed broken $VERSION test.

Now compares against the last commit when doing 'git diff', rather than
against the index. (The test would report the wrong thing if 'fix' was
staged, but not yet commited.)
Now use base64 encoded checksums in state store.

Switched from hex checksums (40 characters long) to base64 checksums (27
characters long).
Option parse errors reported separately.

Instead of gathering up all errors before quitting, option related
errors are now reported separately. Only if option parsing succeeds does
fix go on to report other errors.
Wrote milestone for version 1.0 in TODO.
Added version number to state store.

Fix now detects if its state store has changed its format and throws an
error rather than trying to stupidly build anyway.