Don't rely on checkout being within 'src' folder.

This allows git mirrors like mine to work without the
needless extra level of nesting:

https://github.com/samclegg/naclports

Also, correct directory names in README and add
a .gitignore.

Review URL: https://codereview.chromium.org/11617013

git-svn-id: http://naclports.googlecode.com/svn/trunk/src@650 7dad1e8b-422e-d2af-fbf5-8013b78bd812