Hi Sergey ,
Whether the stow manual mandates/suggests a given layout was analyzed here [0].
The workflow you describe is not the only one possible and the app list is not mandatory. Only when -d is used, please look at my e-mail.
Anyway, if the current implementation works with your directory layout could you please share your home-dotfiles-configuration?
I don't seem to be able to make this implementation work with my layout.
Thank you,
giacomo
[0]:
https://issues.guix.gnu.org/60521#13