The HCDU Plus application is my attempt to remedy these. it reports conflicts at the resource (BHAV, BCON and STR#) level and not at the package level (it's usually enough to know that 'InTeenimater_FlavorPak_BackToSchool.package' conflicts with 'InTeenimater_B.package' without giving the eleven resources that conflict).it can't be told to ignore known conflicts (eg all the InTeenimater flavour paks).
it can't be told which folder to start in.it doesn't consider STR#, OBJD, OBJf or other resources.The Hack Conflict Detection Utility (HCDU) is an essential tool when using mods, but it does have some shortcomings