Add command line flags to better control which files trigger a build.

-exclude-dir=... can be used to block the .git directories from being
processed. The .git directories contain enough files to overrun the
default open file limit of OS X.

-exclude=... can be used to block certain file basename patterns, such
as .#* which is an emacs temporary file which keeps the suffix of the
original file, and thus trips the ordinary pattern selector.

-include=... can be used like the -pattern, but it uses glob matching
which is easier to escape properly from Bourne shell.
Use non-breaking hyphens in README.md

The command options wrap in an ugly way without this.
Clear up some logic
Tighten up an if statement
Merge pull request #4 from jimstudt/exclusions

Exclusions and inclusions