A configuration information manager monitors attempts by processes to update non-structured storage of system configuration information, such as plain text files which contain system configuration information. When such an attempt is made, the configuration information manager makes a copy of the target file, and redirects the write operation to this copy. The configuration information manager then analyzes the process that did the writing, as well as the content that was written. If the process and/or the content is deemed to be suspicious, the changes will be logged and discarded, thus protecting the system. Should the changes be deemed legitimate, then the configuration information manager folds them into the real file, typically in an annotated manner, so as enable subsequent reversion of the changes as desired.