When wanting to consolidate shared parts within your BOM, from the Projects dropdown click on Consolidate. This will open up the Consolidate List modal.
You can choose from the dropdown to consolidate parts by either a shared "Internal Part Number" or the "Manufacturer Part Number", and then click on Consolidate to finish.
Then your shared parts by IPN/CPN or MPN, depending on your selection, will be consolidated within your BOM.