Added permissions fixing after running scratch-copy and implemented a new module

[victor5lm]

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (black and flake8).
• If a new tamplate was added make sure:
  • Template's schema is added in templates/services.json.
  • Template's pipeline's documentation in assets/reports/md/template.md is added.
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PR description

This PR addresses #212.

With the changes implemented in this PR, we make sure that all folders and files copied from scratch to services_and_collaborations have the correct permissions. Furthermore, a fix-permissions module has been added to the tools so that, by providing the absolute path to a folder, all its subfolders and files have the appropriate permissions. This way, when necessary, this module can be ran so that new folders or files have the permissions they should have to avoid any issues.

[saramonzon]

Looks really good! Just some comments that i think will improve performance! But check it in any case