Cert: Add directory structure to genrule

* The generated Python directory need to overlap with the GD source
  directries for them to run together in one ACTS test
* Since both generated library and source library has Python modules
  with the same name, such as "cert", they must not have duplicate
  files for them to be imported in the same interpreter

Bug: 150321998
Test: source cert/run
Change-Id: I2bd4e3e9c3a5ec8d51e0bbba7f8a8a767f9ce866