I have a project with autotools: automake, autoconf.
I want to prohibit make from remaking files configure, Makefile.in, etc;
Try to explicitly tell make those files should not be remade, via command-line
$ make -o configure -o Makefile.in
or by using MAKEFLAGS
$ MAKEFLAGS="-o configure -o Makefile.in" make
The excerpt from GNU make's manual
‘-o file’
‘--old-file=file’
‘--assume-old=file’
Do not remake the file file even if it is older than its prerequisites, and do not remake
anything on account of changes in file. Essentially the file is treated as very old and
its rules are ignored. See Avoiding Recompilation of Some Files.
If yours autotools template correctly uses $(MAKE) for subdirs, there should be no problems.