various fixes to deploy-doc.sh

various fixes to deploy-doc.sh, including NOT converting the link

`https://github.com/SitePen/dstore/blob/master/README.md`

into

`https://github.com/SitePen/dstore/blob/master/README.html`

Also made it more resilient to directories already existing.

PS: Eventually the .md --> .html extension conversion should be done using jekyll filters rather than shell scripts.   Modify all the _layouts/*.html files to say:

```
{{ page.content | convertLinks }}
```

and then define that convertLinks filter as something like https://github.com/bdesham/pluralize/blob/master/pluralize.rb.

So this is somewhat of a temporary solution.