Refactor configuration

[safl]

Currently all configuration-file items have a top-level identifier e.g. fio, qemu, etc. This clashes a bit with the configuration-items for cijoe itself, e.g. the configuration of cijoe-transports has top-level item transport. For example, for the configuration-content:

[transport.ssh]
username = "root"
password = "root"
hostname = "localhost"
port = 4200

This could be under top-level item cijoe. e.g.:

[cijoe.transport.ssh]
username = "root"
password = "root"
hostname = "localhost"
port = 4200

This will align nicely with the recent addition of specifying env and shell for cijoe.run, which looks like:

[cijoe.run]
shell = "csh"
env = {FOO = "bar", JAZZ= "tazz"}