Mostly removes unnecessary use of `extraPkgs = pkgs: appimageTools.defaultFhsEnvArgs.multiPkgs pkgs;`
This caused some packages to be listed twice.
Also, fix some styling, and accidental use of top-level packages (sometimes due to the `with;` keyword, e.g. on `beeper`).
Remove inclusions of `bash`, since `bashInteractive` is already present by default.
The nixpkgs-unstable channel's programs.sqlite was used to identify
packages producing exactly one binary, and these automatically added
to their package definitions wherever possible.
