Integrate configuration searches into engine loading

internal/engine/load.go

@@ -202,6 +202,7 @@ func executeLoadRequest[T any](request loadRequest[T], secrets SecretBinding, lo
 	}
 	accumulator.versionState = versionState
 	input, diagnostics := assembleBaseInputTrackedWithVersion(request.main.source, mainOptions, request.main.destination, accounting, nil, nil, versionState)
+	request.main.source = input.source
 	accumulator.sources = input.sources
 	accumulator.add(versionState.diagnostics...)
 	reportedVersionDiagnostics := len(versionState.diagnostics)