Are numbered headings in Markdown / Rdiscount possible?

If your markdown tool supports customized theme by CSS, add below snippet into CSS to enable heading number:

body {
    counter-reset: h1
}

h1 {
    counter-reset: h2
}

h2 {
    counter-reset: h3
}

h3 {
    counter-reset: h4
}

h1:before {
    counter-increment: h1;
    content: counter(h1) ". "
}

h2:before {
    counter-increment: h2;
    content: counter(h1) "." counter(h2) ". "
}

h3:before {
    counter-increment: h3;
    content: counter(h1) "." counter(h2) "." counter(h3) ". "
}

h4:before {
    counter-increment: h4;
    content: counter(h1) "." counter(h2) "." counter(h3) "." counter(h4) ". "
}

I use Typora, which supports auto numbering for headings in this approach.

Yes, try Pandoc. This works for me:

pandoc --number-sections < test.md > out.html

(Source)

Markdown to produce the numbered outline you mention in the original post looks like this:

# My top-level topic

## My first subtopic

## Another subtopic

### A sub-subtopic

## Another top-level topic

If you want deeper indenting for sub-sections, you might be able to achieve this with inline CSS. For example, placing this at the top of the above Markdown source indents the headers:

<style type="text/css">
  h2 { margin-left: 10px; }
  h3 { margin-left: 20px; }
</style>

But say you had paragraphs of text under your headings... I don't know how to indent that to the same level as the above header.

Update 2015-10-18: Markdeep has numbered headings (and many other fancy features). Check that out too!