Adapt SourceKit LSP plugin to Swift 6

See merge request GNOME/gnome-builder!823

The symbolic icons were previously installed to `scalable/apps`,
when they're expected to be in `symbolic/apps` by services like
apps.gnome.org. This commit ensures they're installed correctly.

The `.desktop` prefix is deprecated, and using it throws a warning
in the [app
overview](https://sophie-h.pages.gitlab.gnome.org/app-overview/?annotations=true&last_review=true&repo_name=true&SEARCH=builder).

Fixes for app overview

See merge request GNOME/gnome-builder!824

I wish we had a better place to do this, but this is easy enough for now
and fixes a realy strange issue where you can't format a python3 document
on save.

If the manifest manually sets the config opt, do not override it.

Related: #2257

Fixes: #2257

That way we can include it internally.

Fixes: #2258

Related: #2259

This needs to be applied to all "flatpak build ..." commands and ensure
that we bind the property as late as possible (when creating the Run
Context) so that any changes in preferences are applied.

Additionally this fixes the value we're setting for FLATPAK_CONFIG_DIR.

Fixes: #2259

Fixes: #2244

Related: #2039

The git plugin is one of the two last holdouts still using signals on the
buffer directly. We want this to use the new commot notify API we added to
GtkTextBuffer instead.

Related: #2039