steps/linux/flatpak: Respect `-y` flag

[har7an]

when deciding whether the -y argument should be added to an operation. Previously the -y was implicitly assumed for regular updates but was ignored for the cleanup steps.

Now, it is added as defined in the topgrade runtime configuration.

Standards checklist:

• [x] The PR title is descriptive.
• [x] The code compiles (cargo build)
• [x] The code passes rustfmt (cargo fmt)
• [x] The code passes clippy (cargo clippy)
• [x] The code passes tests (cargo test)
• [x] Optional: I have tested the code myself
  • [x] I also tested that Topgrade skips the step where needed

If you developed a feature or a bug fix for someone else and you do not have the means to test it, please tag this person here.

[s34m]

Merged at new fork because of inactivity by maintainer.