Update internal documentation

Followup to issue #56.

The [doc](https://github.com/G-Node/gin-cli/tree/master/doc) directory of this repository is meant to include information about the internals of gin-cli such as:
- What git and git-annex commands are called by each gin command
- The package structure of the repository
- Configuration options (in git and git-annex) that the gin client sets and expects (see also [this page](https://web.gin.g-node.org/G-Node/Info/wiki/GinUsageTutorial#using-git-and-git-annex-directly) on the GIN wiki)