Wiki fetching + various fixes

Three major features here:

1. Fetching of wikis for repos when --include-wikis is provided. This is a little nasty because they're not fully supported in the github API and they can fail to clone when not initialized.

2. Fetching over ssh when -s|--ssh is provided. Commit @aa97992 provides justification.

3. Reading of the token from a file. This allows not passing the token on the command line where it can easily be seen from /proc, logs or jenkins. Default is ~/.config/ghtoken, but it can be specified with -t|--token-file.

Besides that, a couple cleanups for system_exec and a fix for duplicate json fetching.