fix(query-planner-js): Strip application of directives from the API schema, not just their declarations

Entire context of this issue is captured by a comment left on a previous PR: https://github.com/apollographql/federation/pull/622#discussion_r603669506

Following the recommended suggestion in that comment broke a bunch of tests (presumably because there's a dependence on these AST nodes in various places) so this may not be trivial or even possible.

Start with the discussion on pull request #622, especially the referenced comment, then reproduce the recommended change and inspect the tests it breaks. Done means directives are stripped from the API schema rather than only their declarations, while the affected query-planner tests pass.

Written by the indexing model from the issue text.