Write merged input yaml to output dir

[lrobion]

Part 3 of #99, merged input files are written to the output directory as merged-input.yaml. This allows tracking of what parameters were used to run APCEMM with 2 caveats:

• Relative paths remain relative even though the location they are relative to is not the same anymore. This is not "incorrect" as it is exactly what was passed to APCEMM but misleading. This can be bundled as a fix with Incorrect relative path resolution when passing multiple input.yaml #116 by resolving all relative paths and recording that in the merged-input.yaml
• If Force seed value = F then APCEMM generates a random seed based on a unix timestamp. The merged-input.yaml does not record this seed and just copy/pastes the merged value in the input files. I kept this as is for now because right now the merged-input.yaml is a record of what was passed to APCEMM. If we want it to be a record of what APCEMM ran with then it would make sense to record the seed in the dedicated yaml field and flip force seed to true, such that re-running APCEMM with merged-input.yaml actually fully reproduces the simulation. Depends on what exactly we want this file to be