Refactor to reflect website structure

[nippoo]

We should have:

/index.html # nice phy homepage
/index.css # nice phy global CSS
/doc/index.md # homepage for the doc (currently readme.md)
/doc/***.md # other markdown doc files
/doc/doc-style.css # documentation/markdown-specific CSS
/doc/gen.php # doc generation script
/install/linux/latest.sh
/install/mac/latest.sh
/install/windows/latest.bat

Untracked on git:

/doc/api/***.md # autogenerated
/install/unix-latest.tar.gz
/install/windows/latest.exe (autobuild)

[rossant]

+1 to all except

/doc/gen.php # doc generation script

haaaaaaaaaaaaa