Situation 11 - Program is installed (v1.0) this includes file X.2 - User modifies file X.3 - Update to v1.1 released, an update to file X is included in patch.* What happens to the user changed file X?
wyUpdate detects the changed file and downloads the catch-all update.
Situation 21 - Program is installed (v1.0) this includes file X.2 - User modifies file X (part of the install).3 - Update to v1.1 released, file X has not changed in update.* Does wyUpdate detect a change to file X?* Does wyUpdate redownload the last patch to include file X?
If file X is not changed in the update, then wyUpdate blissfully ignores the file (whether it was changed by the user or not).
May I ask when your users is changing these files? Are they changing config files? What behavior do you expect?