make distclean should clean up all files created by configure and make.
These files are left behind currently:
aclocal.m4 autom4te.cache build-aux/compile build-aux/config.guess build-aux/config.sub build-aux/depcomp build-aux/install-sh build-aux/ltmain.sh build-aux/m4/libtool.m4 build-aux/m4/lt~obsolete.m4 build-aux/m4/ltoptions.m4 build-aux/m4/ltsugar.m4 build-aux/m4/ltversion.m4 build-aux/missing build-aux/test-driver configure doc/man/Makefile.in Makefile.in src/config/bitcoin-config.h.in src/config/bitcoin-config.h.in~ src/Makefile.in src/secp256k1/aclocal.m4 src/secp256k1/autom4te.cache src/secp256k1/build-aux/compile src/secp256k1/build-aux/config.guess src/secp256k1/build-aux/config.sub src/secp256k1/build-aux/depcomp src/secp256k1/build-aux/install-sh src/secp256k1/build-aux/ltmain.sh src/secp256k1/build-aux/m4/libtool.m4 src/secp256k1/build-aux/m4/lt~obsolete.m4 src/secp256k1/build-aux/m4/ltoptions.m4 src/secp256k1/build-aux/m4/ltsugar.m4 src/secp256k1/build-aux/m4/ltversion.m4 src/secp256k1/build-aux/missing src/secp256k1/build-aux/test-driver src/secp256k1/configure src/secp256k1/Makefile.in src/secp256k1/src/libsecp256k1-config.h.in src/secp256k1/src/libsecp256k1-config.h.in~ src/univalue/aclocal.m4 src/univalue/autom4te.cache src/univalue/build-aux/compile src/univalue/build-aux/config.guess src/univalue/build-aux/config.sub src/univalue/build-aux/depcomp src/univalue/build-aux/install-sh src/univalue/build-aux/ltmain.sh src/univalue/build-aux/m4/libtool.m4 src/univalue/build-aux/m4/lt~obsolete.m4 src/univalue/build-aux/m4/ltoptions.m4 src/univalue/build-aux/m4/ltsugar.m4 src/univalue/build-aux/m4/ltversion.m4 src/univalue/build-aux/missing src/univalue/build-aux/test-driver src/univalue/configure src/univalue/Makefile.in src/univalue/univalue-config.h.in src/univalue/univalue-config.h.in~
Ubuntu 16