./configure/make in subdir?

Does anyone know if it's possible to persuade ./configure to work from within subdirs? I keep flipping back and forth between master and v2.1.x and it would be nice to be able to re-use builds without having to have two git repos & associated hassles. I've seen syntax like this work on some projects. git checkout v2.1.x cd build-v21x ../configure --prefix=/opt/fr21x make make install cd .. git checkout master cd master ../configure --prefix=/opt/frmaster make make install ...but this seems to fail on (the accursed!) libltdl subdir "configure" which is apparently jumping back up into the top-level source directory. I suspect it would similarly fail on the module configure scripts too.