I think that transformations should be applied to `-D --file' combination as well (probably to `-D --manifest' too).
It would support the following use case (this is the reason I fould this very bug). When we have a project under development which is controlled by guix.scm file and we want to try out the dependency from another fork or branch, it would be useful for transformations to be propagated to inputs/propagated-inputs/etc. inside guix.scm file. Currently it doesn't apply transformations: --8<---------------cut here---------------start------------->8--- guix shell -D -f guix.scm \ --with-git-url=python-pytelegrambotapi=https://github.com/coder2020official/pyTelegramBotAPI \ --with-branch=python-pytelegrambotapi=polling-improvements --8<---------------cut here---------------end--------------->8--- However it does propagate: --8<---------------cut here---------------start------------->8--- guix shell -f guix.scm \ --with-git-url=python-pytelegrambotapi=https://github.com/coder2020official/pyTelegramBotAPI \ --with-branch=python-pytelegrambotapi=polling-improvements --8<---------------cut here---------------end--------------->8--- and this, when dependency is mentioned explicitly: --8<---------------cut here---------------start------------->8--- guix shell -D -f guix.scm python-pytelegrambotapi \ --with-git-url=python-pytelegrambotapi=https://github.com/coder2020official/pyTelegramBotAPI \ --with-branch=python-pytelegrambotapi=polling-improvements --8<---------------cut here---------------end--------------->8---