Make all file operations through the filesystem interface

[jsoriano]

What does this PR do?

Migrate all the pending file operations to be done through the filesystem interface.

Why is it important?

This will allow to validate the spec on packages that are stored on any resource for what an implementation of the filesystem interface is available.

This will be also useful to mock filesystems that can be used for testing some scenarios, like the ones needed for #278.

Checklist

• I have added test packages to test/packages that prove my change is effective. No test added, but as a refactor I focused on making the current ones pass.
• I have added an entry in versions/N/changelog.yml. No user facing change.

Related issues

• Useful to test Implement package limits #278.

[elasticmachine]

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• Start Time: 2022-02-23T15:28:02.688+0000

• Duration: 4 min 21 sec

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[jsoriano]

@mtojek sorry, I have just pushed a function to validate zips, happy to move this to a different PR, I only wanted to try this with a different implementation of fs.FS.