Links to GitHub ".md" files changing to links to non-existent ".html" equivilents

[JohnMount]

For GitHub projects with a README.md (or README.Rmd) links that happen to link to ".md" files in the same GitHub project get converted from ".md" to ".html" during pkgdown::build_site() (and are thus broken as pkgdown is not in a position to produce those ".html" files). This is happening to links that are not part of the doc-tree and thus should not be translated. My guess is pkgdown thinks these are links under its management (thinks they are pointing into the doc area and need to change to ".html") when they are links to un-related sections of the package/project.

Minimal example explaining the issue here.

A work-around is to relpace ".md" with "%2Emd" to hide the links from the processor.

[hadley]

i.e. tweak_md_links() should check only modify relative paths, not paths that have a protocol.