update docs/add warning when conf settings defined in package.py are ignored

Only a subset of the config settings are actually used if redefined in a package.py. For example, those affecting the resolve (packages_path etc) are ignored, because by the time the package.py is read, the resolve is already underway.

The docs should more clearly describe this, and these settings should be detected in package.py's and produce a warning to the effect that they're being ignored.

Start by locating the documentation describing configuration settings and the package.py loading path. Compare settings used during resolve with settings read afterward, then define the warning behavior for ignored settings. Done means the documentation clearly explains the limitation and package.py definitions of those settings produce a warning.

Written by the indexing model from the issue text.