When using gEDA some components are ignored by the ratsnest. How should this be handled?
Instead of editing the symbol, you can accomplish the same effect using slots feature. Add the following attributes to the transistor: slot=1 numslots=1 slotdef=1:3,2,1

Numbers in slotdef after 1: represent package pin numbers, in pinseq order. In the example above, for npn-3 symbol, C has pinseq=1 and will be assigned pin 3, B has pinseq=2 and will be assigned pin 2, and E has pinseq=3 and will be assigned pin 1.

Other transistors may have different pin assignments. For example,  use slotdef=1:2,1,3 for an MJE305 in TO220W package. If you keep editing the symbol you will keep breaking your previous designs. You can also create a bunch of clones with different pin assignments, but that can get out of hand pretty quickly if you use many different types of transistors.