The wyBuild 2.6.x and below make what we call "direct patches". That is, the patches are from every old version to the latest version.
This is why (among other reasons) we say to add all files into wyBuild. Let wyBuild decide which files to patch, which files to delete, and which files to add.
In wyBuild 2.7.x we're adding the ability to make incremental patches (e.g. 1.1 -> 1.2, 1.2->1.3, etc.).