relative paths all the way?

build.ninja

...

build CMakeFiles/blah.dir/main.cpp.o: CXX_COMPILER__blah ../main.cpp
  DEP_FILE = CMakeFiles/blah.dir/main.cpp.o.d
  OBJECT_DIR = CMakeFiles/blah.dir
  OBJECT_FILE_DIR = CMakeFiles/blah.dir
  
...

CMakeLists.txt

cmake_minimum_required(VERSION 3.6)

project(blah)

add_executable(
    blah
    main.cpp
)

gistfile1.txt

cmake -G Ninja /path/to/cmake-problem

rules.ninja

...

rule CXX_COMPILER__blah
  depfile = $DEP_FILE
  deps = gcc
  command = /usr/bin/c++   $DEFINES $INCLUDES $FLAGS -MD -MT $out -MF $DEP_FILE -o $out -c $in
  description = Building CXX object $out
  
...