The ability to call random external programs during the build of your project is not a feature, it's a bug. Likewise the ability to lay out your source arbitrarily. Your project's build is not a unique and special snowflake; it can build the same way as every other project, the way that has already been tried and tested by millions, the way that any developer will immediately understand.
If there's really some step that needs to be done in your builds that isn't covered by the existing plugins, you can write your own (it's not hard) and then at least that step is happening in a structured, testable way. But if you're doing something unique to a single project, you shouldn't be doing it in the build system.
> Your project's build is not a unique and special snowflake; it can build the same way as every other project, the way that has already been tried and tested by millions, the way that any developer will immediately understand.
No, actually, builds can get very unique in multi-language systems or in embedded systems... believe me. =)
If there's really some step that needs to be done in your builds that isn't covered by the existing plugins, you can write your own (it's not hard) and then at least that step is happening in a structured, testable way. But if you're doing something unique to a single project, you shouldn't be doing it in the build system.