You can clone with
HTTPS or Subversion.
I discovered that piwik monitoring will not work if the piwik webserver is not available on https.
Configuring HTTPS is not so simple and assuming that if the monitored server is using HTTPS the same is valid for piwiki is a bad assumption.
Also even when HTTPS is configured if the certificate does not validate the monitoring will fail.
Another issue is performance, https does request additional load for both client and server, load that may not be desired.
By default piwik should work even if the server is available only on http://.
Unfortunately, this is a web server configuration issue and outside of Piwik's scope.
If the web site being tracked is using https, you can't expect browsers to respect the non-SSL tracking.
Your options are: