Cherry-pick #23456 to 7.x: Skip top level files when unziping archive during upgrade

[michalpristas]

Cherry-pick of PR #23456 to 7.x branch. Original message:

What does this PR do?

Fixes codepath for top level files which was completely incorrect.

Why is it important?

Upgrade working properly, without this it leads to incorrect paths generation and target files wont be found

Checklist

• My code follows the style guidelines of this project
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have made corresponding change to the default configuration files
• I have added tests that prove my fix is effective or that my feature works
• I have added an entry in CHANGELOG.next.asciidoc or CHANGELOG-developer.next.asciidoc.

[elasticmachine]

Pinging @elastic/ingest-management (Team:Ingest Management)

[blakerouse]

Backport looks good.

[elasticmachine]

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Build stats

• Build Cause: Pull request #23458 updated

• Start Time: 2021-01-12T18:45:32.948+0000

• Duration: 22 min 37 sec

Test stats 🧪

Test	Results
Failed	0
Passed	1410
Skipped	6
Total	1416

💚 Flaky test report

Tests succeeded.

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Test stats 🧪

Test	Results
Failed	0
Passed	1410
Skipped	6
Total	1416