[docs] Update language regarding repository vs package root

[docs] Update language regarding repository vs package root

In the current documentation, there are many places with language that
assumes a *repository* (as in VCS) is the same as *package root* (the
directory where `Cargo.toml` sits).

With the new workspace features, this is far from true now, and the
inaccurate language makes it difficault for newbies or developers
without much familiarity with the cargo internals with authoring their
manifest files.

This diff tries to use the right terms for places any of these concepts
is referred to:

* Package root,
* Workspace root,
* VCS repository, and
* Package repository/index, like crates.io.