I have a project directory structure of:
Root
Source
Common
MyFolder
++ My 3 source files and header
When I am building
This is sort of counter to how makefiles and cmake usually work.
Most users consider it really important that make performs an incremental build.
The usual way with makefiles is to do make clean which is supposed to remove any binaries and object files that were created.
However, sometimes I write cmake scripts that use globbing over the source directory to assemble the project. (That means, it says "just grab all *.cpp files in the /src folder and make an executable from them".) A makefile cannot check what files in a directory, so the make build will be broken after I add a new file, and make clean won't fix it -- the whole makefile will need to be regenerated by cmake.
Usually what I do is, I write a simple bash script, named rebuild.sh or something,
#!/bin/bash
rm -rf build
mkdir build
cd build
cmake ..
make -j3
./tests
And I put that in the root of my repository, and add /build to my .gitignore. I call that when I want to do a full rebuild -- it nukes the build directory, so its foolproof. When I want an incremental rebuild, I just type make again in the /build directory.
The rebuild.sh script can also serve a double purpose if you use travis-ci for continuous integration.