There doesn't seem to be a specific option to place modules in (.dat, .msg files) during the configure process. It seems to be hardcoded to the lib directory.
This creates some packaging issues as certain packagers desire to place only dynamic or static libs in the lib folder and place the modules elsewhere.
Would it be possible to have an option to set the modules directory from the configure script inside the source3 folder? Thanks!
3.6 will not see any changes like that. No stable branch will see changes like that actually. Have a look at master. Only the waf build is supported since 4.1 days. I think you will find all you need here though, like with --datadir etc. you will be able to just have libs in lib. modules are libs actually, this is why I found parts of your request a bit confusing.