These files are often updated by me and i want to be sure that users are using the latest versions of them. But if fact, wyUpdate performs things another way!
That's not exactly true. Here's how wyBuild builds the updates (let's say from version "A" to version "B"):
If the file exists in both versions
wyBuild compares them. If they're identical wyBuild excludes them from the update (wyUpdate won't touch the file at all during the update). If they're different wyBuild generates a patch.
If the file exists in version "A" but not in version "B"
wyBuild will delete the file.
If the file exists in version "B" but not in version "A"
wyBuild will include the full file.
how to make wyUpdate compare files and update them if the latest versions of files are availible?
It does this by default. Perhaps I'm misunderstanding. Can you give me an example of where this is failing? (Also, you might want to check out the video intro to wyBuild/wyUpdate/AutomaticUpdater - it quickly covers a lot of the errors new users make.)