Add "depth" column to the discarded_edgelist

[ptajvar]

This PR adds a "depth" column to the discarded edgelist as it enables easier downstream analysis to understand the multiplet recovery process.

The recovered_components file will also be removed as an output of the GRAPH step. The recovered_components file stores the refinement history and is no longer needed as it can be easily recovered from discarded edgelist. We can backtrack to a given refinement depth by bringing in the edges that are removed after that depth. If we merge all of the edges from discarded_edgelist to edgelist we will recover the COLLAPSE output.

Fixes: EXE-2046

Type of change

Please delete options that are not relevant.

• Breaking change (fix or feature that would cause existing functionality to not work as expected)

How Has This Been Tested?

Unit tests, and tried on a V2 sample.

PR checklist:

• This comment contains a description of changes (with reason).
• I have performed a self-review of my own code
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have checked my code and documentation and corrected any misspellings
• I have documented any significant changes to the code in CHANGELOG.md

[ambarrio]

LGTM

[ludvigla]

Looks great!