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    copied!<p>The following is still work in progress, but I think I am on the right track. I started with the following (standard) directory structure, in which I want to include a git c++ project:</p> <pre><code>+---src +---main +---c++ +---java </code></pre> <p>Because I do not want to change the directory structure of the original make project, I needed to define the custom source directory and a custom include directory. This is the resulting directory structure after a pull (I left out irrelevant file structures):</p> <pre><code>+---src +---main +---c++ +---data +--- ... +---examples +--- ... +---scripts +--- ... +---src +---hunalign +--- ... (source files) +---include +--- ... (header files) +---utils +--- ... (helper classes) +---tools +--- ... </code></pre> <p>With the following configuration I got the project compiled.</p> <pre><code> &lt;build&gt; &lt;plugins&gt; &lt;plugin&gt; &lt;artifactId&gt;maven-nar-plugin&lt;/artifactId&gt; &lt;version&gt;2.1-SNAPSHOT&lt;/version&gt; &lt;extensions&gt;true&lt;/extensions&gt; &lt;configuration&gt; &lt;libraries&gt; &lt;library&gt; &lt;type&gt;executable&lt;/type&gt; &lt;run&gt;true&lt;/run&gt; &lt;/library&gt; &lt;/libraries&gt; &lt;!-- Here is the config for the custom source dir and includes --&gt; &lt;cpp&gt; &lt;sourceDirectory&gt; ${basedir}/src/main/c++/src/hunalign &lt;/sourceDirectory&gt; &lt;includes&gt; &lt;include&gt;${basedir}/src/main/c++/src/include/*.h&lt;/include&gt; &lt;/includes&gt; &lt;/cpp&gt; &lt;libraries&gt; &lt;library&gt; &lt;type&gt;executable&lt;/type&gt; &lt;run&gt;true&lt;/run&gt; &lt;/library&gt; &lt;/libraries&gt; &lt;/configuration&gt; &lt;/plugin&gt; &lt;/plugins&gt; &lt;/build&gt; </code></pre> <p>EDIT: to make javah run properly, I had to symlink it, as maven kept looking in the wrong place for it:</p> <pre><code>sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.7.0_13.jdk/Contents/Home/bin/javah /Library/Java/JavaVirtualMachines/jdk1.7.0_13.jdk/Contents/Home/jre/bin/javah </code></pre>
 

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