Method and system for managing software conflicts and a computer-readable storage medium having a program for executing the method is provided wherein a database of interrelated tables is utilized. The invention may be used to manage file and registry conflicts on Windows desk tops. The invention determines information about changes made by applications during their installation into a computer system, one application at a time. Those changes are then compared to determine which files and other shared resources conflict with one another. This conflict information is then used to attempt to resolve software conflicts. Conflicts can be identified at many different levels: files, registries, shortcuts, ODBC drivers, ODBC data sources, service, device, components, autoexec.bat, config.sys, INI changes, and paths. This invention stores all information needed to recreate the installation in the database itself. Thus, when changes (i.e. when conflicts between multiple applications are being resolved) are made to the database, a needed installer for that application can be generated. The database categorizes all file types and breaks the information down into manageable tables of information. These tables relate to each other in an intricate web that allows a thorough illustration of files.