Refreshing a merge module's file system references

I'm regularly facing the problem that my merge module's references get out of sync with the file system. Between two builds, the content of some directories changes. Some开发者_StackOverflow中文版 files get removed and some new ones appear. Is there a way to automatically refresh these references so the merge module is in sync with the file system?

Windows Installer XML (Wix) is a solution.