I just added a section to the documentation: 
http://coapp.org/reference/autopackage-ref.html

How to have Include files nested in a subfolder
Sometimes the package creator wants to have files placed in a subdirectory so 
that consuming developers includes files like:
// sample include
#include <mylib/mylib.h>
Autopackage tries to un-nest as much as possible. To work around this you can 
add a different file section and tell it how to add the files to the package:
nuget {
    files {
        // instead of using something like this:
        include {
            "inc\*.h"
        };

        // use this:
        nestedInclude {
            #destination = ${d_include}\mylib;
             "inc\*.h"
        };
    };
};
This will copy the files into the subdirectory of the include folder.



From: Coapp-developers 
[mailto:coapp-developers-bounces+garretts=microsoft....@lists.launchpad.net] On 
Behalf Of n...@gmx.net
Sent: Thursday, May 23, 2013 1:42 AM
To: coapp-developers@lists.launchpad.net
Subject: [Coapp-developers] How to placed files in subdirectory of include path

Hi all,

I am new to the CoApp project, and try to make a c++ template lib available as 
nuget package with autopkg.

The include files are structured in subdirectories, but when I place them in 
the .autopkg file,
they appear only in a flat structure include directory. Here is the files part 
of the .autopkg file

  files {
    include : { "inc\*.h", "inc\armadillo_bits\*.hpp" };

    [x86, v110, debug] {
      lib: "bin\Debug\*.*";
    }

    [x86, v110, release] {
      lib: "bin\Release\*.*";
    }

All files form inc\*.h and inc\armadillo_bits\*.hpp goes into the flat 
directory include.
But I would like to see them in include\armadillo_bits.

best regards
  nhok
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