patch a file which is created while a phase is running which otherwise fails?

[ng0]

How can I achieve this?

For multiple packages I have this happens:

Application setup launches into configure or build phase, some script
creates a file where the creation process can not be located easily
asuming that a "#! /bin/sh" as shebang and/or "/bin/sh" as executable
somewhere in the file will just work and our build system says "¡No
pasarán!"...

So I was thinking, Guile is flexible, it should be achievable to have
something which wraps itself around the phase and for a new file it just
patches in what you throw at it in advance. Of course I'm open for
whatever works before we get to this.

Examples I can think off my head are the mach buildsystem used by the
firefox deriviate palemoon, pike (as far as I know, been some time since
I made progress on this one).

Thanks
-- 
              ng0