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Strange output in STM32CubeMX Ver 4.12.0

Question asked by Rob on Jan 22, 2016
I recently upgrade CubeMX to version 4.12.0 and used it to generate code for a custom STM32F407VGT board. Everything seemed to work fine with previous versions, but not so much with the latest version. For example...

There is no function generated for MX_DMA_Init() in "main.c", even though there is a function prototype at the top of the file. This of course occurs when the DMA controller is enabled in CubeMX

The file "stm32f4xx_it.h" is not generated when it should be.

In "usbd_conf.c", there is a line generated near the top of the file that just contains a #n. Nothing else, just "#n"

There are a huge number of errors in the "USBD_LL_Init()" function in the "usbd_conf.c" file. There's text in this file which has no business being there at all. Here's a copy/paste of some of that text:

Java backtrace for programmers:
freemarker.template.TemplateException: Error reading included file Src/usb_otg_fs_HalInit.tmp
     at freemarker.core.Include.accept(
     at freemarker.core.Environment.visit(
     at freemarker.core.MixedContent.accept(
     at freemarker.core.Environment.visit(
     at freemarker.core.ConditionalBlock.accept(
     at freemarker.core.Environment.visit(
     at freemarker.core.MixedContent.accept(