I don't think there is any .htaccess in the build, appart from the one in config/ that is there for security purposes and should not suffer / overwrite a configuration.
The robots.txt is necessary otherwise the error.log/access.log gets full of 404 errors when bots try to load the robots.txt which has been an issue reported by several users in the past.
Quite right, I forgot ./.htaccess wasn't under version control.
re: robots,txt. I agree it's convenient, but the flip side is that (a) unzipping into an existing installation will overwrite local mods and (b) it isn't used when piwik is installed in a subfolder, eg http://example.com/piwik