> Question is:  What do you use to version control permission sensitive
files?  Subversion doesn't give a damn about permissions, so even after I
clean up this mess, I think I should probably
> avoid it.

We use Puppet to make sure managed files have proper ownership, permissions
and relevant services are automatically reloaded whenever files change.
Files are kept in versioning on the Puppet server.

file { "/etc/rsyslog.conf":
  ensure => file,
  source => '/path/to/file',
  owner => 'root',
  group => 'root',
  mode =>  '0644',
  notify => Service['rsyslog'],
}

Best,

Hans
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