How can I make custom commands and targets flush their output immediately instead of waiting until the end when using the Ninja generator?

When I build using ninja on windows the output of some commands is only written to the console when the command finishes.

For example if I run docker under ninja there is some output but there is not for doxygen. So it could be that the two commands are behaving differently and this is not a ninja issue at all.

The only discussion about this I can find is: https://github.com/ninja-build/ninja/issues/545
It suggests that using a console pool it might be possible somehow.
I have tried things like:

set NINJA_STATUS="[%s/%t] %es %b (%ds)"
ninja -v -d stats -d keeprsp -j 1

to no avail.

The clue is here in the ticket you linked to.

> Starting in CMake 3.2, you can use USES_TERMINAL (or JOB_POOL console starting in 3.15, but preferably the first one) option of add_custom_command() to specify Ninja uses the console pool.

add_custom_target(run_doxygen ALL
    COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile 
    COMMAND echo > ${CMAKE_BINARY_DIR}/Doxyfile.ok
    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
    COMMENT "Generating developer documentation with Doxygen"
    JOB_POOL console
    VERBATIM )

This helps when using CMake.
In the build.ninja file, JOB_POOL results in pool = console.