Fix permission issue for newly created dirs/files in install_scripts.sh

[bedroge]

This issue surfaced when building the init dir for the new 2025.06 version, and only on Deucalion: the permissions on the init/bash and modules/EESSI/2025.lua files were wrong, and didn't have read permissions for others. I suspect it's related to the default umask on Deucalion (?).

I noticed that install_scripts.sh already used a special procedure in sed_update_if_changed (see https://github.com/EESSI/software-layer-scripts/blob/main/install_scripts.sh#L58), which explicitly sets the umask and uses cat for copying the files (apparently to retain the permissions?). This PR uses the same approach for copying missing/modified files (instead of using cp). #37 (comment) shows that this solves the issue on Deucalion.

[gpu-bot-ugent]

Instance eessi-bot-vsc-ugent is configured to build for:

• architectures: x86_64/amd/zen3
• repositories: eessi.io-2023.06-compat, eessi.io-2023.06-software, eessi-hpc.org-2023.06-software, eessi-hpc.org-2023.06-compat

[casparvl]

Looks good to me

[gpu-bot-ugent]

PR merged! Moved [] to /scratch/gent/vo/002/gvo00211/SHARED/trash_bin/EESSI/software-layer-scripts/2025.07.15