Machina no Kiseki ~Ogeretsu Daihyakka Gaiden~

Main character is a skilled steam mechanic engineer living in the town of Greenock. He lives in the local church orphanage with autonomous android Iris.
One day they learn that church is about to be demolished. Protagonist needs to raise a large sum of money to save his home. Together with Iris and nun Unia they take up a job of deciphering the contents of ancient books and create devices by the sketches.

[From vndbreview]