run: Break out generation of run flags from context to helper

This also adds a call to this from flatpak build, although it is
not (yet) strictly necessary as all the flags it sets so far
are always set when building. This may change in the future though.

Closes: #1721
Approved by: alexlarsson
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Gitea Version: 1.28.0+dev-477-g8b6ad49a5f