Output has wrong extension
I'm getting files with md formatting, but extensions are still .html
Eg: My index.html, NOT index.md looks like this (markdown):
It's very easy to make some words **bold** and other words *italic* with Markdown. You can even [link to Google!](http://google.com)
Sometimes you want numbered lists:
1. One
2. Two
3. Three
Sometimes you want bullet points:
* Start a line with a star
* Profit!
Alternatively,
- Dashes work just as well
- And if you have sub points, put two spaces before the dash or star:
- Like this
- And this
If you want to embed images, this is how you do it:

Seems to be related to https://github.com/TypeStrong/typedoc/issues/237
Ok yeah, I see that theme.js is supposed to take care of exensions and its not being called by typedoc > 0.3.12
I worked around this in case you're intereted: https://github.com/thepalebluedot/typedoc-md-theme
I have the same issue.
And it seems that the new line in markdown files is missing.
@thepalebluedot I tried your branch, the extension is ok. However, I feel the output content need to be more refined.
Hi,
I agree with zixia - the extensions are correct but the {{newLine}} expansion does not seem to "trigger" the handlebars helper. The markdown is correct except for newlines, which makes it close but not quite usable.
I think it is this helper that is not running:
handlebars.registerHelper('newLine', function () { return '\n'; });
Any ideas as to why this function is not called by the {{newLine}}s in the templates would be greatly appreciated.