Errors reproducing examples in the Wiki

[Coloquinte]

I used the docker image to run the example in the Wiki. There are minor changes to be made with the Wiki example usage:

• the generated netlist now ends with nl.v everywhere, not netlist.v,
• the simulations run requires a clock argument (fault -c Tech/osu035/osu035_stdcells.v -v 100 -r 50 -m 95 --ceiling 1000 Netlists/s27.nl.v.cut.v --clock CK)
• the bench export command complains about the presence of inout ports on PADINOUT (workaround is to remove it from the library).
• the command errors out with the help message when using the --bench argument for Atalanta: fault -g atalanta -c Tech/osu035/osu035_stdcells.v -b Netlists/s27.nl.v.cut.v.bench Netlists/s27.nl.v.cut.v

[donn]

Looking into them- I'll also just move the documentation to just readthedocs because it turns out GitHub wikis aren't great