documentation and relative path

I added the options.md file to the main page, because a lot of the comments in the "Issues" of this project could be answered from there.

I added back the process.cwd replace that had been removed.  The use case is when a project has multiple index.js files, because they're using node's require to include entire directories.  (i.e., the metalsmith project does this a lot).

I also creates quick links from the top of the options markdown to the rest of the file, because having two big lists in the same file confuses github.