First reported at
https://cygwin.com/ml/cygwin/2015-05/msg00140.html

I was not able to bisect make code to identify when
the issue was introduced.
Attached test case

--- original message ----

Using 32-bit cygwin 2.0.2 and make 4.1-1, in a recipe, redirecting
stderr in append mode does not work if the program being invoked on a
shell line is a native Windows executable.  Instead of appending, the
stderr output is written to the top of the file, corrupting it. This
happens only if the 'make' process has its own stdout/err redirected to
a pipe.

Example recipe:

    all:
            echo first > output
            echo
secondxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> output
            /cygdrive/c/Windows/System32/sort.exe nonexist 2>> output; true

When "make" is run, the "output" file should be:

    first
    secondxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    nonexistThe system cannot find the file specified.

and in fact it is.  But when "make 2>&1 | cat" is run, the output is:

    nonexistThe system cannot find the file specified.
    xxxxxxxxxxxxxx

even though it should be the same as before.  The error message written
by sort.exe went to the top of the file instead of the end.

The problem does not happen if 'sort.exe' is replaced with a cygwin
program such as /usr/bin/sort.

The problem does not happen if stdout is redirected instead of stderr.

The problem does not happen if the output of 'make' is redirected to
a file instead of a pipe.

The problem does not happen if the sequence of commands in the recipe
is copied into a shell script and the shell invoked with its output
redirected to a pipe.  That is why I am filing this against 'make'.
However, it is possible the bug is in the shell (or a different shell?)
and I just don't know how to invoke it properly to imitate what 'make'
does.

I am attaching a reproducer Makefile.  Run "make 2>&1 | cat" to see
the incorrect output:

    $ make 2>&1 | cat
    echo first > output
    echo secondxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >>
output
    /cygdrive/c/Windows/System32/sort.exe nonexist 2>> output; true
    ----- BEGIN output -----
    nonexistThe system cannot find the file specified.
    xxxxxxxxxxxxxx
    ----- END output -----

The bug happens with both make 4.1 and make 4.0 on cygwin 2.0.2.  It
does not happen with make 3.82.90 and cygwin 1.7.23.