Git clone functionality fixes

[filippomc]

Follows up from #720, relates to CH-37

The paths were not correctly relativized when used inside a top level app. Also codefresh paths needed fix.

Implemented solution: fixed paths

How to test this PR: same as #720

Sanity checks:

• [x] The pull request is explicitly linked to the relevant issue(s)
• [x] The issue is well described: clearly states the problem and the general proposed solution(s)
• [x] From the issue and the current PR it is explicitly stated how to test the current change
• [x] The labels in the issue set the scope and the type of issue (bug, feature, etc.)
• [x] All the automated test checks are passing
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Breaking changes (select one):

• [x] The present changes do not change the preexisting api in any way
• [ ] This PR and the issue are tagged as a breaking-change

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Test coverage (select one):

• [x] Tests for the relevant cases are included in this pr
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Nice to have (if relevant):

• [ ] Screenshots of the changes
• [ ] Explanatory video/animated gif