Improve documentation

[senderle]

This is a big issue with lots of potential sub-issues. Ideas:

• Provide details about required metadata structure, viz. that the first column must be filenames, the filenames in the metadata must match the actual filenames exactly, but can be extended paths as long as the files are all in the same folder and the matches are exact.
• Give more detailed help for the individual fields and options.
• Add contextual information to the HTML output.
• Duplicate and extend the existing (but stale and hard-to-find) documentation on the wiki branch. (And then delete that branch!)

Feel free to add to this list.

[senderle]

Related: #53