Complete AMC recovery with the full clocks reset sequence

Description

This MR aims at enabling the complete clock reset sequence on the back-end board.

Related Issue

How Has This Been Tested?

One can start a run after resetting all the clocks in the right order. All MGT links are also reset properly.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.