Source-Files are a type of persistent upgrade that is more powerful than Augmentations. Source-Files are received by destroying a Bitnode. There are many different BitNodes in the game and each BitNode will grant a different Source-File when it is destroyed.
A Source-File can be upgraded by destroying its corresponding BitNode a second or third time (playing through that BitNode again). It can be upgraded to a maximum of level 3, with the exception of Source-File 12, which has no hard limit.