Run commands in prefix, not cwd

In general, we should never be relying on {cwd}/package.json.

The current working directory should be used for printing out relative
paths for human consumption, but npm should always walk up the directory
tree to find its working dir for *doing* stuff.

Fix #6059
npmconf@2.0.7

Support -C as an alias for --prefix.
npm-registry-client@3.1.7

Clean up auth logic and improve logging around auth decisions. Also
error on trying to change a user document without writing to it.
update changelog for npm@2.0.0-beta.2
2.0.0-beta.2
changelog cleanups