Update format script
Auto-format entire site

Ignored:

* index.html
* function-aliases.md
* spatial-jdbc.md
* OpenJUMP.md
Fix special cases
Merge pull request #375 from agouge/auto-format

Auto format the entire website

To give it a consistent look-and-feel. Uses my format script.
There were some exceptions and special cases that I had to take care of manually.