config: tweak ruby configs to clean up hierarchy

Re-enabling implicit parenting (see previous patch) causes current
Ruby config scripts to create some strange hierarchies and generate
several warnings.  This patch makes three general changes to address
these issues.

1. The order of object creation in the ruby config files makes the L1
   caches children of the sequencer rather than the controller; these
   config ciles are rewritten to assign the L1 caches to the
   controller first.

2. The assignment of the sequencer list to system.ruby.cpu_ruby_ports
   causes the sequencers to be children of system.ruby, generating
   warnings because they are already parented to their respective
   controllers.  Changing this attribute to _cpu_ruby_ports fixes this
   because the leading underscore means this is now treated as a plain
   Python attribute rather than a child assignment. As a result, the
   configuration hierarchy changes such that, e.g.,
   system.ruby.cpu_ruby_ports0 becomes system.l1_cntrl0.sequencer.

3. In the topology classes, the routers become children of some random
   internal link node rather than direct children of the topology.
   The topology classes are rewritten to assign the routers to the
   topology object first.

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