fix(libnpmexec): fix read mixed local/registry pkg

Refactor / clean up of the logic around reading installed
packages. Fixes reading packages from mixed sources (one being
from the local installed tree and the other from the registry
using pacote.manifest).

Makes it so that libnpmexec is always reading from the
Arborist actual tree instead of reading `node_modules` from
the file system when retrieving local package data.

Fixes: npm#3668
Relates to: npm#4643
Relates to: npm#4619
Relates to: npm/statusboard#403