Bazel docs infra: stop naively converting all markdown links to html

The jekyll build script below naively converts all .md links in the doc site to .html. This is desirable for most links since the doc site uses .html in URLs, but it has caused problems when the intention is to keep the .md extension. For example, when linking directly to markdown files on GitHub.

https://github.com/bazelbuild/bazel/blob/357282fa857a007555ae053afc827283a3e402d6/site/jekyll-tree.sh#L104-L111

Start with site/jekyll-tree.sh lines 104-111, where Markdown links are converted during the Jekyll documentation build. Trace how the script distinguishes links intended to remain .md from links that should become .html. Done means the build preserves direct Markdown links while retaining the existing conversion for normal documentation links.

Written by the indexing model from the issue text.