Made suitable for running as a system service

A change long overdue. Previously, Hydrogen Proxy made several
assumptions which made it difficult or hackish to run as a system
service. This commit:
 * Makes the configuration directory (previously $HOME/.hydrogen_proxy)
   configurable via a command line option.
 * Makes the configuration directory disableable via a command line
   option.
 * Makes the settings module configurable via a command line option.
 * Makes the certificate locations configurable via the settings file.
 * Recreates the hydrogen_mkcert and hydrogen_clearcerts scripts in
   Python and allows them to access the settings module to determine
   certificate locations as necessary.
 * And probably a few other things.

This commit also removes Bash as a dependency (except possibly when
using the SubprocessModifyingHandler?) which theoretically improves
portability to Windows.

This commit breaks backwards-compatibility in one way. It moves the
default root certificate location from
$HOME/.hydrogen_proxy/certs/root/ca.pem to $HOME/.hydrogen_proxy/ca.pem
and the default server private key location from
$HOME/.hydrogen_proxy/certs/root/ckey.pem to
$HOME/.hydrogen_proxy/ckey.pem . If you've been running an older version
of Hydrogen Proxy, you can fix this with the following commands:

 > mv ~/.hydrogen_proxy/certs/root/ca.pem ~/.hydrogen_proxy/ca.pem
 > mv ~/.hydrogen_proxy/certs/root/ckey.pem ~/.hydrogen_proxy/ckey.pem
 > rmdir ~/.hydrogen_proxy/certs/root