As mentioned before (see Entry Points) the entry point functions all perform a global diff of your project just after having prepared the mail buffer. There might be times, however, when you want to work on a project subset only (a specific set of files or directories), for instance in order to commit only a few of the current changes. This concept is know to Patcher as working on a “subproject”.
A subproject is essentially defined by the project on which it is based, an optional subdirectory in which the whole subproject resides and an optional set of specific files to work on, in that subdirectory.
Warning: for technical reasons (and also because right now I don't want to clutter Patcher's code too much with workarounds for deficient RCSes), it is not possible to define Mercurial subprojects with a specific subdirectory. This problem will go away when issue 2726 is resolved (http://mercurial.selenic.com/bts/issue2726).
When you provide an explicit set of files to work on, it is not necessary (it is even forbidden) to specify the ChangeLog files. Patcher will automatically find them for you. In other words, only specify source files, not ChangeLog files.
Patcher offers to ways of working on subprojects: either temporarily or by defining them in a permanent fashion.