Remove application.js after bundle in template

[taylor-steve]

Fixes part of #3014. I believe the manifest.js issue is fixed, but unreleased, in blacklight-gallery so that would still require manually fixing that newline if testing this for real.

Moves the removal of app/javascript/application.js to the end of the end of the process. Steps that run after the install_generator, like stimulus-rails installing, recreate the file.

https://github.com/hotwired/stimulus-rails/blob/ae4b675473b71fdf01530c8a6a3bb277d3388ee2/lib/install/stimulus_with_importmap.rb#L11