Maintain unified alt src invariant on atom select

internal/gps/solver.go

@@ -1253,8 +1253,15 @@ func (s *solver) selectAtom(a atomWithPackages, pkgonly bool) {
 		}
 
 		if len(newp) > 0 {
+			// If there was a previously-established alternate source for this dependency,
+			// but the current atom did not express one (and getting here means passed the source
+			// hot-swapping rules - see checkIdentMatches()), then we have to create the new bmi
+			// with the alternate source. Otherwise, we end up with two discrete
+			// project entries for the project root in the final output, one with
+			// the alternate source, and one without. See #969.
+			id, _ := s.sel.getIdentFor(dep.Ident.ProjectRoot)
 			bmi := bimodalIdentifier{
-				id: dep.Ident,
+				id: id,
 				pl: newp,
 				// This puts in a preferred version if one's in the map, else
 				// drops in the zero value (nil)