Organizing Chef cookbooks Is it 100% required to store all the cookbooks under chef-repo? This seems a little bit inconvenient for me, I'd prefer to store solution cookbooks in the application codebase, or just as a standalone git repos.

I know that tools like knife rely on configuration files to be present in .chef, and it frustrates me a little bit too.
No, it is not, the chef-repo is the legacy way back to chef 10.

Knife allows working on multiples directory with the -o option. Berks work from current directory.

You can also work around the default .chef directory by using the KNIFE_HOME environment variable too. 

The current recomendations is indeed a repo per cookbook (or alongside another app)