Please add the below code in the beginning of main.c of your application project.
mainTimer = 0u;
CyGlobalIntEnable; /* Enable global interrupts. */
Now it should work.
I have added the above code ,Still in the same state, it is not working.
Additional to response#1, you have to add the custom linker script for your bootloadable project as well and have to give the correct path for same to Linker ( Build Setting).
Attached is the modified working project build with PSoC Creator 4.2 with GCC 5.4.1 toolchain.
The project is build for 128KB devices,for 256 K devices modify the linker script file as per this document - http://www.cypress.com/file/198301/download page#47.
You said "Attached is the modified working project" but there is no attachment. The link leads to an app note, but not a project.