Probably it's not a fault of repos but installer's defaults. When you create your first domain manually instead of using installer to generate domain1 often some additional configuration is needed.
It's too late to think what was your problem last year. Solution for your problem was and is:
instead of calling
$ asadmin start-domain --domaindir /home/alpha/glassfishv2/ --user alpha --passwordfile /home/alpha/glassfishv2/toilet/password.txt toilet
perform one time (to generate ~/.asadminpass)
$ asadmin login
and than simply
$ asadmin start-domain --domaindir /home/alpha/glassfishv2 toilet
best regards,
artur
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