It might have something to do with wiring_pulse.c which seems to be here:
C:\Program Files (x86)\Arduino\hardware\arduino\cores\arduino
While there is also a wiring_pulse.S in the newer version

:
C:\Program Files (x86)\Arduino_1-6-8\hardware\arduino\avr\cores\arduino
Note that the paths are different.
It seems that the error in the tool build arises from the presence of the following files in the folder:
C:\Program Files (x86)\Arduino_1-6-8\hardware
platform.txt:
# ctags
# ------------------------------
tools.ctags.path={runtime.tools.ctags.path}
tools.ctags.cmd.path={path}/ctags
tools.ctags.pattern="{cmd.path}" -u --language-force=c++ -f - --c++-kinds=svpf --fields=KSTtzns --line-directives "{source_file}"
# additional entries
tools.avrdude.path={runtime.tools.avrdude.path}
preproc.includes.flags=-w -x c++ -M -MG -MP
preproc.includes.compatibility_flags={build.mbed_api_include} {build.nRF51822_api_include} {build.ble_api_include} {compiler.libsam.c.flags} {compiler.arm.cmsis.path} {build.variant_system_include}
recipe.preproc.includes="{compiler.path}{compiler.cpp.cmd}" {preproc.includes.flags} -DF_CPU={build.f_cpu} -DARDUINO={runtime.ide.version} -DARDUINO_{build.board} -DARDUINO_ARCH_{build.arch} {compiler.cpp.extra_flags} {build.extra_flags} {preproc.includes.compatibility_flags} {includes} "{source_file}"
preproc.macros.flags=-w -x c++ -E -CC
preproc.macros.compatibility_flags={build.mbed_api_include} {build.nRF51822_api_include} {build.ble_api_include} {compiler.libsam.c.flags} {compiler.arm.cmsis.path} {build.variant_system_include}
recipe.preproc.macros="{compiler.path}{compiler.cpp.cmd}" {compiler.cpreprocessor.flags} {compiler.cpp.flags} {preproc.macros.flags} -DF_CPU={build.f_cpu} -DARDUINO={runtime.ide.version} -DARDUINO_{build.board} -DARDUINO_ARCH_{build.arch} {compiler.cpp.extra_flags} {build.extra_flags} {preproc.macros.compatibility_flags} {includes} "{source_file}" -o "{preprocessed_file_path}"
and platform.keys.rewrite.txt:
old.0.compiler.path={runtime.ide.path}/hardware/tools/avr/bin/
new.0.compiler.path={runtime.tools.avr-gcc.path}/bin/
old.1.tools.avrdude.cmd.path={runtime.ide.path}/hardware/tools/avr/bin/avrdude
new.1.tools.avrdude.cmd.path={path}/bin/avrdude
e.conf
new.2.tools.avrdude.config.path={path}/etc/avrdude.conf
14q1/bin/
new.3.compiler.path={runtime.tools.arm-none-eabi-gcc.path}/bin/
old.4.tools.bossac.path={runtime.ide.path}/hardware/tools
new.4.tools.bossac.path={runtime.tools.bossac.path}
old.5.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" {compiler.c.elf.flags} -mcpu={build.mcu} "-T{build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" {compiler.c.elf.extra_flags} -o "{build.path}/{build.project_name}.elf" "-L{build.path}" -mthumb -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -Wl,--start-group "{build.path}/syscalls_sam3.c.o" {object_files} "{build.variant.path}/{build.variant_system_lib}" "{build.path}/{archive_file}" -Wl,--end-group -lm -gcc
new.5.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" {compiler.c.elf.flags} -mcpu={build.mcu} "-T{build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" {compiler.c.elf.extra_flags} -o "{build.path}/{build.project_name}.elf" "-L{build.path}" -mthumb -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -Wl,--start-group "{build.path}/core/syscalls_sam3.c.o" {object_files} "{build.variant.path}/{build.variant_system_lib}" "{build.path}/{archive_file}" -Wl,--end-group -lm -gcc
#specific to RedBearLab nRF51822 Boards
old.6.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" -mcpu={build.mcu} -mthumb -Wl,--gc-sections --specs=nano.specs -Wl,--wrap,main -Wl,-Map={build.path}/{build.project_name}.map,--cref "-T{build.variant.path}/{build.ldscript}" -o "{build.path}/{build.project_name}.elf" -Wl,--start-group "{build.path}/system_nrf51.c.o" {object_files} "{build.path}/startup_NRF51822.s.o" "{build.path}/{archive_file}" -Wl,--end-group -lstdc++ -lsupc++ -lm -lc -lgcc -lnosys
new.6.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" -mcpu={build.mcu} -mthumb -Wl,--gc-sections --specs=nano.specs -Wl,--wrap,main -Wl,-Map={build.path}/{build.project_name}.map,--cref "-T{build.variant.path}/{build.ldscript}" -o "{build.path}/{build.project_name}.elf" -Wl,--start-group rf51.c.o" {object_files} "{build.path}/core/startup_NRF51822.S.o" "{build.path}/{archive_file}" -Wl,--end-group -lstdc++ -lsupc++ -lm -lc -lgcc -lnosys
#specific to RFduino 1.6.3
old.7.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" {compiler.c.elf.flags} -mcpu={build.mcu} {build.extra_flags} "-T{build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" -Wl,--cref -o "{build.path}/{build.project_name}.elf" "-L{build.path}" -Wl,--warn-common -Wl,--warn-section-align -Wl,--start-group "{build.path}/syscalls.c.o" {object_files} "{build.variant.path}/{build.variant_system_lib}" "{build.variant.path}/libRFduino.a" "{build.variant.path}/libRFduinoBLE.a" "{build.variant.path}/libRFduinoGZLL.a" "{build.path}/{archive_file}" -Wl,--end-group
new.7.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" {compiler.c.elf.flags} -mcpu={build.mcu} {build.extra_flags} "-T{build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" -Wl,--cref -o "{build.path}/{build.project_name}.elf" "-L{build.path}" -Wl,--warn-common -Wl,--warn-section-align -Wl,--start-group "{build.path}/core/syscalls.c.o" {object_files} "{build.variant.path}/{build.variant_system_lib}" "{build.variant.path}/libRFduino.a" "{build.variant.path}/libRFduinoBLE.a" "{build.variant.path}/libRFduinoGZLL.a" "{build.path}/{archive_file}" -Wl,--end-group
old.8.recipe.ar.pattern="{compiler.path}{compiler.ar.cmd}" {compiler.ar.flags} {compiler.ar.extra_flags} "{build.path}/{archive_file}" "{object_file}"
new.8.recipe.ar.pattern="{compiler.path}{compiler.ar.cmd}" {compiler.ar.flags} {compiler.ar.extra_flags} "{archive_file_path}" "{object_file}"
old.9.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" {compiler.c.elf.flags} -mcpu={build.mcu} "-T{build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" {compiler.c.elf.extra_flags} -o "{build.path}/{build.project_name}.elf" "-L{build.path}" -mthumb -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--start-group "{build.path}/syscalls_sam3.c.o" {object_files} "{build.variant.path}/{build.variant_system_lib}" "{build.path}/{archive_file}" -Wl,--end-group -lm -gcc
new.9.recipe.c.combine.pattern="{compiler.path}{compiler.c.elf.cmd}" {compiler.c.elf.flags} -mcpu={build.mcu} "-T{build.variant.path}/{build.ldscript}" "-Wl,-Map,{build.path}/{build.project_name}.map" {compiler.c.elf.extra_flags} -o "{build.path}/{build.project_name}.elf" "-L{build.path}" -mthumb -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--start-group "{build.path}/core/syscalls_sam3.c.o" {object_files} "{build.variant.path}/{build.variant_system_lib}" "{build.path}/{archive_file}" -Wl,--end-group -lm -gcc
#specific to Digistump AVR Boards 1.5.4
...
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