You can just create a PCB with one additional layer and use that layer (top one for example if you make single-sided pcbs at home) for jumpers, then to add a ju

You can just create a PCB with one additional layer and use that layer (top one for example if you make single-sided pcbs at home) for jumpers, then to add a jumper while routing a trace, switch layers, which will add a through-hole via, trace your jumper, then jump back to the initial layer through another via. When etching the board you omit that layer and later solder wires where the traces were. It's quite flexible as you can add jumpers of any length and orientation that way, the only inconvenient is that jumpers aren't marked on the silkscreen but it's fine for home-made projects.