This is tricky since in this situation you prefer not to have an extension on your symlink, and there's no reliable way that I know of to automatically detect a markdown file based on its syntax (since it is after all intended to be human-readable without rendering), so
ftdetect is out of the picture. However, you do have some options.
If you tend to make similarly named symlinks to Markdown files, you can add an
autocommand to set the filetype for you when reading these files:
" Your autocmds should be defined inside a group and cleared at the start so
" that they are not defined more than once if you happen to re-source your vimrc.
" See http://learnvimscriptthehardway.stevelosh.com/chapters/14.html
" If you have other files that you always want to use Markdown syntax, add them
" after 'Note' below, comma delimited. Some other ideas could be README, AUTHORS,
" CONTRIBUTING, COPYING, etc
autocmd BufNewFile,BufRead Note setf markdown
Or, you can use a
modeline. I do not believe that there is an official syntax for Markdown comments, but I've seen most support basic HTML comments. So you could append this to your Markdown file:
<!-- vim: set ft=markdown: -->
:h modeline for the full details on this feature. N.B. this will not show up in the rendered Markdown, so long as the implementation supports comments, which most that I've seen do indeed.