Library resolution... Header files resolved by library priority order. The same header (.h) can now exist in more than one library. #include the most import library headers first into a sketch so that the correct version of duplicates will be found. 

For example: a file called SPI.h exists with a header called Test.h in a user library (folder) called Test. If the sketch code #includes <Test.h> and <SPI.h> then the SPI.h will be used from the Test library/folder. If the sketch code does not #include <Test.h>, then the SPI.h is used from the Arduino Ide SPI library.

tip: If manual changes to the sketch #includes are made then saving an .ino source code file or compiling the project will force intellisense path resolution/update.