Allow for multiple absolute directories as separate API docs in one project

[mvriel]

With phpDocumentor it had been possible in the past to provide multiple folders to parse and phpDocumentor would try to find a common folder as 'project root' and considered these provided folders to be part of the same project.

With the changes that we are doing in phpDocumentor 3, it would make more sense to interpret multiple (absolute) folders as separate API sections (loose components if you will) in the config and treat those as DSNs.

For this to work, we need to make changes in the way we convert command-line options to the configuration but it would improve the way multiple -d arguments are handled.

In addition, it should be possible for configuration API sections to have a specified subfolder instead of trying to render it all in one, and templates should support multiple API sections.

[mvriel]

This is not a blocker for release of v3.0; pushing this to 3.1