title: cmake builds the whole project when touching CMakeLists.txt in a subdir
body: <p>I have a quite large <code>c++</code> project with lots of dependencies. If I have to change something in the <code>CMakeLists.txt</code> of one application's subdirectory (nothing else depends on this), on my PC only this application is rebuilt, as expected.</p>
  
  <p>When I do the same thing on the target system, the whole project gets rebuild. After generation, I see that the <code>flags.make</code> and <code>link.txt</code> in almost all subdirectories have the current timestamp, while on the PC only those in the said directory have been touched.</p>
  
  <p>PC and target run a Debian with <code>cmake 3.0.2</code> and use the same configuration; there are just some different flags when <code>$ARCH</code> is <code>armhf</code>.</p>
  
  <p>How to proceed to find the cause of this problem?</p>