Allow concordances to be embedded in Markdown output

[dmurdoch]

I am working on a package that will translate locations for error messages about HTML output into locations in the original Rmd file (see https://github.com/dmurdoch/RmdConcord). With current knitr, it can only convert locations to the intermediate Markdown file; this patch will allow knitr to embed enough information in the Markdown intermediate file so that the message can refer back to the original source.

A possible variation on this patch is to remove the format check within concord_mode completely, i.e. to write it as

# do not consider child mode for concordance
concord_mode = function() {
  opts_knit$get('concordance') && !child_mode() 
}

but I think the checks still need to be kept in concord_gen, so they may as well be here.

[dmurdoch]

This is insufficient to handle Rmd -> pdf conversions. I'll improve it and resubmit.

[dmurdoch]

The test for concordances needed to be generalized to handle PDF or LaTeX output.

[yihui]

Looks good to me! Thanks!

A possible variation on this patch is to remove the format check within concord_mode completely, i.e. to write it as

That sounds okay to me. If you want to do it, I'll merge this PR after you are done, otherwise I can also merge it as is.