If you want your project to use the pinmap configuration that you've created, you'll need to adapt the Makefile to point to the correct generated configuration header file, generated from your .gpio file.
The default Makefile uses the board evbe7000p from the E-SDK, we need to replace this name with the name of the generated configuration header file.
The Makefile must contain the correct CONFIG_BOARD variable, and we need to adapt the C_INCS

Here are the two modifications, illustrated in the diff window below. The right part illustrates the default content of the Makefile, while the left part shows the modifications.

Now that the Makefile is updated, you can compile your project, which now points to the good configuration.