Christopher Collins resolved MYNEWT-500.
    Resolution: Fixed

> newt - Ambiguity when package contains two source files with the same filename
> ------------------------------------------------------------------------------
>                 Key: MYNEWT-500
>                 URL: https://issues.apache.org/jira/browse/MYNEWT-500
>             Project: Mynewt
>          Issue Type: Bug
>          Components: Newt
>            Reporter: Christopher Collins
>            Assignee: Christopher Collins
>             Fix For: v1_0_0_rel
> For example, the arduino repo (until very recently) contained the following 
> two files:
> * 
> {{hw/mcu/atmel/samd21xx/src/sam0/utils/cmsis/samd21/source/gcc/startup_samd21.c}}
> * {{hw/mcu/atmel/samd21xx/src/startup_samd21.c}}
> Both of these files are in the same package (hw/mcu/atmel/samd21) and they 
> both have the same filename (startup_samd21c).
> During a build, newt compiles both, but only links in one object file.
> The problem is that the bin directory structure does not mirror that of the 
> source tree.  Specifically, all of a package's object files get put in the 
> same directory; subtrees are not preserved.  Consequently, the second .o file 
> overwrites the first.
> The fix is to preserve the source directory structure in the bin directory.

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