Using File Filters you can define which project files belong to your documentation and have to be checked. You can include and exclude, both folders and files, using ANT pattern syntax. Your project will be checked if any files are missing or are new when you start i-net Doqua or change the configuration.
The ant-like syntax of the filter criteria looks like:
The example shows:
htmlfiles in every folder of the project
index.htmlfiles and everything in the (root!) folder