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In the beta wikipedia projects, the site_domain column looks improperly populated with just a "."

stdClass Object
(
    [site_id] => 13
    [site_global_key] => hewiki
    [site_type] => mediawiki
    [site_group] => wikipedia
    [site_source] => local
    [site_language] => he
    [site_protocol] => 
    [site_domain] => .
    [site_data] =>
a:1:{s:5:"paths";a:2:{s:9:"file_path";s:36:"//he.wikipedia.beta.wmflabs.org/w/$1";s:9:"page_path";s:39:"//he.wikipedia.beta.wmflabs.org/wiki/$1";}}
    [site_forward] => 0
    [site_config] => a:0:{}
)

it should be something like site_domain: gro.skoobikiw.fa.  Note that I ran the populate sites table script with the --strip-protocols option.