set umask when Genome is loaded

This seems bold but I don't know how else to deal with user's custom
umask's that restrict results.
remove code that is trying to restore "default permissions"

It is believed these were trying to work around issues with umask and
setgid "not working" but instead we should try to fix the problem.
use Genome::Sys->rename instead of CORE::rename

Genome::Sys->rename does not preserve permissions, user, and group so
respects setgid which is usually desired.
return instead of die
mimic CORE::rename better

Since CORE::rename doesn't throw exception change this to not either.
Which means some existing uses need to throw exceptions again to match
previous CORE::rename usage.

Check known error conditions CORE::rename produces and mimic by setting
$! and returning false.
restore exceptions removed when Genome::Sys->rename threw exceptions
towards making permissions work correctly in CLE and Research