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nRF5 SDK 12.0.0, Undefined symbol app_uart_init

I am trying to re-base my SDK package, and when I started off with the ble_app_template project for the pca10040 s132, I copied my main file on top, everything compiles just fine except for the following error messages:

.\_build\nrf52832_xxaa.axf: Error: L6218E: Undefined symbol app_uart_get (referred from main.o).
.\_build\nrf52832_xxaa.axf: Error: L6218E: Undefined symbol app_uart_init (referred from main.o).
.\_build\nrf52832_xxaa.axf: Error: L6218E: Undefined symbol app_uart_put (referred from main.o).

I have confirmed that app_uart.h is included at the top of main.c, I have checked that components\libraries\uart is included in my paths. I have nrf_drv_uart.c and app_uart_fifo.c as part of the project files which corresponds to the uart_pca10040 project example, and I have also tried includeing app_uart.c as part of the project files.

No matter what I do, I cannot avoid this error, and I can right click on the include statement, and navigate down the header file to the declaration and find it right there.

I am so confused why it doesn't see it.

Side note, I did a clean targets in the project menu, and it eliminated a bunch of my files in my SDK directories, whats the deal with that.

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