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Codesourcery toolchain under Win7/cygwin can't find some files

I have searched this but the questions I found are about getting the
toolchain to work, my problem is that it works on all but a few
directories.  Also I am not building Linux.

I am trying to move a project from a Linux machine to Windows to make
people happy.  The same project builds fine under Linux (Ubuntu 12.04)
using the Linux Binary for the same toolchain (I recently reloaded
both toolchains from the same directory at Mentor to be sure, see
details below).

I installed Cygwin, got the packages, set up paths, etc.  In general
the build works for 90% of the project BUT as make traverses the
directory, it finds everything except two files (to clarify, these two
are the first files in their respective directories, so I assume the
problem will apply to the whole directory).  The log below shows the
first fail:

 - if I take lwip out of the build then it blows up on the next one

 - if I take the next one out of the build then everything else (quite
a bit) compiles; then the linker fails on the two missing items as

More precisely, e.g.
it finds  /home/Nadi/project/version-2.9/external/freertos/Source/portable/GCC/ARM_CM3_MPU/port.c

but not /home/Nadi/project/version-2.9/external/lwip/src/api/api_lib.c
from the directory that I am running make, "ls" finds the file that
the compiler cannot.

    $ make
     [cc] Debug/api_lib.o
     arm-none-eabi-gcc.exe: error:
/home/Nadi/project/version-2.9/external/lwip/src/api/api_lib.c: No
such file or directory
     arm-none-eabi-gcc.exe: fatal error: no input files compilation terminated.
     Makefile:189: recipe for target `Debug/api_lib.o' failed
     make[2]: *** [Debug/api_lib.o] Error 1
     Makefile:37: recipe for target `lwip_world' failed
     make[1]: *** [lwip_world] Error 2
     Makefile:160: recipe for target `extern' failed
     make: *** [extern] Error 2

 - GCC Chain : arm-none-eabi-gcc ; gcc version 4.7.2 (Sourcery
CodeBench Lite 2012.09-63)
  - Cygwin    : CYGWIN_NT-6.1-WOW64

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