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

[trevor-scheer]

Entire context of this issue is captured by a comment left on a previous PR: #622 (comment)

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.

[pcmanus]

I'm 99.9% sure this isn't a problem anymore in the federation 2 code. Do we want to keep this open for the version-0.x branch?