Symlinks make in-tree builds look like out-of-tree builds

[d-torrance]

Describe the bug
If we run the configure script from a symlinked directory but call configure using the non-symlinked path (or vice versa), then flint compiles correctly, but fails at the linking step:

/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_new_mpz':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:86: multiple definition of `_fmpz_new_mpz'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:86: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo:(.tbss+0x8): multiple definition of `mpz_free_num'; build/fmpz/fmpz.lo:(.tbss+0x8): first defined here
/usr/bin/ld: build/fmpz/fmpz.lo:(.tbss+0x10): multiple definition of `mpz_free_arr'; build/fmpz/fmpz.lo:(.tbss+0x10): first defined here
/usr/bin/ld: build/fmpz/fmpz.lo:(.tbss+0x0): multiple definition of `mpz_free_alloc'; build/fmpz/fmpz.lo:(.tbss+0x0): first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_clear_mpz':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:145: multiple definition of `_fmpz_clear_mpz'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:145: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_cleanup_mpz_content':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:195: multiple definition of `_fmpz_cleanup_mpz_content'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:195: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_cleanup':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:223: multiple definition of `_fmpz_cleanup'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:223: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_promote':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:230: multiple definition of `_fmpz_promote'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:230: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_promote_val':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:242: multiple definition of `_fmpz_promote_val'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:242: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_demote_val':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:256: multiple definition of `_fmpz_demote_val'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:256: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_init_readonly_mpz':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:280: multiple definition of `_fmpz_init_readonly_mpz'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:280: first defined here
/usr/bin/ld: build/fmpz/fmpz.lo: in function `_fmpz_clear_readonly_mpz':
/tmp/symlink-to-flint/src/fmpz/fmpz.c:290: multiple definition of `_fmpz_clear_readonly_mpz'; build/fmpz/fmpz.lo:/tmp/symlink-to-flint/src/fmpz/fmpz.c:290: first defined here
make: *** [Makefile:436: build/fmpz_merged.lo] Error 1

The problem is that we link everything we've compiled in the source directory and the generated file fmpz.c from the build directory. If we call configure using the actual directory from the symlink or vice versa, then we think we're in an out of tree build, and so we end up linking the objects from the generated file twice, since it's really in the same directory.

This is a problem when using spack in macOS since builds are in /var, but that's really a symlink to /private/var.

Steps to reproduce

cd /tmp
git clone https://github.com/flint/flint
ln -s flint symlink-to-flint
cd symlink-to-flint
./bootstrap.sh
/tmp/flint/configure
make
# linking error

Expected behavior

FLINT should link correctly :)

System (please complete the following information):

• System CPU:
• Version of FLINT (if using Git, please specify commit): 58030f4
• How FLINT was configured (i.e. options pushed): /tmp/flint/configure # no additional options
• Output of configure

  $ /tmp/flint/configure
  checking build system type... zen-pc-linux-gnu
  checking host system type... zen-pc-linux-gnu
  checking how to print strings... printf
  checking for gcc... gcc
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables... 
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether the compiler supports GNU C... yes
  checking whether gcc accepts -g... yes
  checking for gcc option to enable C11 features... none needed
  checking for a sed that does not truncate output... /usr/bin/sed
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking for egrep... /usr/bin/grep -E
  checking for fgrep... /usr/bin/grep -F
  checking for ld used by gcc... /usr/bin/ld
  checking if the linker (/usr/bin/ld) is GNU ld... yes
  checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
  checking the name lister (/usr/bin/nm -B) interface... BSD nm
  checking whether ln -s works... yes
  checking the maximum length of command line arguments... 1572864
  checking how to convert zen-pc-linux-gnu file names to zen-pc-linux-gnu format... func_convert_file_noop
  checking how to convert zen-pc-linux-gnu file names to toolchain format... func_convert_file_noop
  checking for /usr/bin/ld option to reload object files... -r
  checking for file... file
  checking for objdump... objdump
  checking how to recognize dependent libraries... pass_all
  checking for dlltool... no
  checking how to associate runtime and link libraries... printf %s\n
  checking for ar... ar
  checking for archiver @FILE support... @
  checking for strip... strip
  checking for ranlib... ranlib
  checking for gawk... gawk
  checking command to parse /usr/bin/nm -B output from gcc object... ok
  checking for sysroot... no
  checking for a working dd... /usr/bin/dd
  checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
  checking for mt... mt
  checking if mt is a manifest tool... no
  checking for stdio.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for strings.h... yes
  checking for sys/stat.h... yes
  checking for sys/types.h... yes
  checking for unistd.h... yes
  checking for dlfcn.h... yes
  checking for objdir... .libs
  checking if gcc supports -fno-rtti -fno-exceptions... no
  checking for gcc option to produce PIC... -fPIC -DPIC
  checking if gcc PIC flag -fPIC -DPIC works... yes
  checking if gcc static flag -static works... yes
  checking if gcc supports -c -o file.o... yes
  checking if gcc supports -c -o file.o... (cached) yes
  checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
  checking whether -lc should be explicitly linked in... no
  checking dynamic linker characteristics... GNU/Linux ld.so
  checking how to hardcode library paths into programs... immediate
  checking whether stripping libraries is possible... yes
  checking if libtool supports shared libraries... yes
  checking whether to build shared libraries... yes
  checking whether to build static libraries... no
  checking for a race-free mkdir -p... /usr/bin/mkdir -p
  checking how to run the C preprocessor... gcc -E
  checking if compiler is GCC... yes
  checking if compiler is Clang... no
  checking for inline... inline
  checking whether byte ordering is bigendian... no
  checking if memory is strongly-ordered... yes
  checking for gmp.h... yes
  checking if version of GMP is greater than 6.2.1... yes
  checking if GMP defines mp_limb_t as unsigned long long int... no
  checking for mpfr.h... yes
  checking if version of MPFR is greater than 4.1.0... yes
  checking for desired ABI... 64
  checking for stdarg.h... yes
  checking for math.h... yes
  checking for float.h... yes
  checking for errno.h... yes
  checking for fenv.h... yes
  checking for alloca.h... yes
  checking for malloc.h... yes
  checking for sys/param.h... yes
  checking for windows.h... no
  checking for pthread_np.h... no
  checking for pthread.h... yes
  checking for library containing atan2... -lm
  checking for library containing __gmpz_init... -lgmp
  checking for library containing __gmpn_mul_basecase... none required
  checking for library containing __gmpn_gcd_11... none required
  checking for library containing __gmpn_div_q... none required
  checking for library containing __gmpn_invert_limb... none required
  checking for library containing __gmpn_modexact_1_odd... none required
  checking for library containing __gmpn_addmul_2... none required
  checking for library containing __gmpn_add_n_sub_n... none required
  checking for library containing __gmpn_add_nc... none required
  checking for library containing __gmpn_sub_nc... none required
  checking for library containing __gmpn_addlsh1_n... none required
  checking for library containing __gmpn_addlsh1_n_ip1... no
  checking for library containing __gmpn_rsh1sub_n... none required
  checking for library containing __gmpn_rsh1add_n... none required
  checking for library containing __gmpn_mulmid_n... none required
  checking for library containing mpfr_init... -lmpfr
  checking for library containing mpfr_round_p... none required
  checking for library containing mpfr_mulhigh_n... none required
  checking for library containing mpfr_sqrhigh_n... none required
  checking whether gcc accepts -pthread... yes
  checking if cpu_set_t is supported... yes
  checking if alloca works... yes
  checking for aligned_alloc... yes
  checking for _aligned_malloc... no
  checking whether gcc accepts -O3... yes
  checking whether gcc accepts -pedantic... yes
  checking whether gcc accepts -std=c11... yes
  checking whether gcc accepts -Wall... yes
  checking whether gcc accepts -Werror=implicit-function-declaration... yes
  checking whether gcc accepts -Werror=newline-eof... no
  checking whether gcc accepts -Wno-stringop-overread... yes
  checking whether gcc accepts -Wno-stringop-overflow... yes
  checking whether gcc accepts -Wmissing-prototypes... yes
  checking whether gcc accepts -Wno-deprecated-declarations... yes
  checking whether gcc accepts -march=znver1... yes
  checking whether gcc accepts -funroll-loops... yes
  checking for immintrin.h... yes
  checking if system have required x86_64 instruction set for fft_small... (cached) yes
  checking if system can use FLINT's fft_small module... yes
  checking for suitable m4... m4
  checking whether assembler supports --noexecstack option... yes
  checking how to switch to text section... .text
  checking how to switch to data section... .data
  checking for assembler label suffix... :
  checking for assembler global directive... .globl
  checking for assembler global directive attribute... 
  checking if globals are prefixed by underscore... no
  checking how to switch to read-only data section... 	.section	.rodata
  checking for assembler .type directive... .type	$1,@$2
  checking for assembler .size directive... .size	$1,$2
  checking for assembler local label prefix... .L
  checking for assembler byte directive... .byte
  checking if .align assembly directive is logarithmic... no
  checking if the .align directive accepts an 0x90 fill in .text... yes
  checking for assembler COFF type directives... no
  creating config.m4
  configure: creating ./config.status
  config.status: creating Makefile
  config.status: creating flint.pc
  config.status: creating src/flint.h
  config.status: creating src/config.h
  config.status: creating src/flint-config.h
  config.status: linking src/gmpcompat.h.in to src/gmpcompat.h
  config.status: linking src/mpn_extras/x86_64/zen3/flint-mparam.h to src/flint-mparam.h
  config.status: linking src/fmpz/link/fmpz_single.c to src/fmpz/fmpz.c
  config.status: executing libtool commands
  

Additional context
Add any other context about the problem here.