title: Automatic dependency generation and compilation in non-flat directory src
body: <p>I'd like to adapt the <a href="http://make.mad-scientist.net/papers/advanced-auto-dependency-generation/" rel="nofollow noreferrer">combined automatic dependency approach</a> to a non-flat directory situation where headers are located under ./include/ and implementation files under ./src/ (while Makefile is in the current directory .). I'd like to hold all intermediate and .d (dependency) files inside a separate directory (potentially separate ./build/ and ./.deps/) . To avoid potential clash for dependency files when more than one file with the same name in different subdirectories of ./include/ and ./src/ can exist, I guess building the same structure as in ./src/ in ./.deps could be a solution.</p>
  
  <p>Apart from adding -I directive to the compile phase in the above linked Makefile, what else should I add? </p>