For some time now, if I run "make clean", it doesn't clean well enough to avoid compile errors. The only thing that seems to work is to completely remove the directories, and re git clone. E.g. after a recent git clean, followed by autogen.sh, followed by configure, followed by make, I get:-
make -C src qt/bitcoin-qt
make[1]: Entering directory /home/rebroad/src/bitcoin/make/src' OBJCXXLD qt/bitcoin-qt /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 0 has invalid symbol index 11 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 1 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 2 has invalid symbol index 2 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 3 has invalid symbol index 2 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 4 has invalid symbol index 11 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 5 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 6 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 7 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 8 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 9 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 10 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 11 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 12 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 13 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 14 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 15 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 16 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 17 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 18 has invalid symbol index 13 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_info): relocation 19 has invalid symbol index 22 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/Scrt1.o(.debug_line): relocation 0 has invalid symbol index 2 /usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu/Scrt1.o: In function_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status