You can clone with
HTTPS or Subversion.
This is not normally a problem for most users since releases do not include the unit tests.
For the benefit of developers, however...
While fixing #896, I noticed version_core in my live database got munged. When I revisited the dashboard, it prompted a database upgrade (from 0.2.9).
Munging of piwik_option table doesn't appear to be reproduceable after #896.
However, API/DocumentationGenerator.test.php continues to access the live database. If possible, this should be changed.
This just bothered me too much...
(In ) fixes #897 - unit tests should not access live database