Merge PBIT files

I am trying to compare differences of 2 PBIT files using ALM toolkit. However, ALM toolkit cannot update a target PBIT file. Do you have any tips how to merge PBIT files or use this for version control? I need to at least merge the datamodelschema of my PBIT files. I have tried the following:

1. Open PBIT file in Tabular Editor > Save as a folder > Open database.json

-Is there a way to convert the database.json to PBIT file without corrupting it so I can open it again in Power BI desktop?

2. Merge changes in ALM toolkit. Below error shows:

I was hoping to at least include PBIT file and JSON datamodelschema in my Git but I am more concerned how I can merge PBIT changes from different branches. 

Thank you!