Fix tools invocation for xdg scripts

[unbel13ver]

The invocations of tools are reworked in a Nix-friendly way.

Checklist for things done

• Summary of the proposed changes in the PR description
• More detailed description in the commit message(s)
• Commits are squashed into relevant entities - avoid a lot of minimal dev time commits in the PR
• Contribution guidelines followed
• Ghaf documentation updated with the commit - https://tiiuae.github.io/ghaf/
• PR linked to architecture documentation and requirement(s) (ticket id)
• Test procedure described (or includes tests). Select one or more:
  • Tested on Lenovo X1 x86_64
  • Tested on Jetson Orin NX or AGX aarch64
  • Tested on Polarfire riscv64
• Author has run make-checks and it passes
• All automatic Github Action checks pass - see actions
• Author has added reviewers and removed PR draft status
• Change requires full re-installation
• Change can be updated with nixos-rebuild ... switch

Instructions for Testing

In gui-vm, double-click on any .pdf file, it should open as usual.

• List all targets that this applies to: x86 Laptop
• Is this a new feature
  • List the test steps to verify:
• If it is an improvement how does it impact existing functionality?
  It does not impact existing functionality but prevents possible future issues.

[brianmcgillion]

Change this to writeShellApplication, then the packages are passed as inputs and you don't need to use app path, just binary name e.g. 'realpath' vs pkgs.coreutils/bin/...