fix confd wait issue

when trying to boot up the registry, it would skip setting etcd
values if anything was set. Because we made some changes to the
cookbook to set some variables to configure the storage backend,
this broke the container. Changing it to set the secretKey if
not present by default fixes the original intention of this
logic.
only write out chef config if necessary, restart based on pid files
fix overlapping bind-mount issues
Merge pull request #646 from opdemand/fix-registry-seed

fix confd wait issue