System Workbench for STM32

I made with CubeMX a very basic project, FreeRTOS, RCC High speed crystal, Low speed disable, sys debug SWD, Timebase TIM1. When I import it and build, I get errors:
Description Resource Path Location Type
Symbol 'SysTick_IRQn' could not be resolved main.c /Disco_emWIN_1/Src line 166 Semantic Error
Description Resource Path Location Type
Symbol 'TIM1_UP_TIM10_IRQn' could not be resolved stm32f4xx_hal_timebase_TIM.c /Disco_emWIN_1/Src line 71 Semantic Error
Description Resource Path Location Type
Symbol 'TIM1_UP_TIM10_IRQn' could not be resolved stm32f4xx_hal_timebase_TIM.c /Disco_emWIN_1/Src line 74 Semantic Error

When I changed optimization to 0, I got more errors, e.g.
GPIO_InitTypeDef GPIO_InitStruct;

/* GPIO Ports Clock Enable */
__HAL_RCC_GPIOC_CLK_ENABLE();
__HAL_RCC_GPIOF_CLK_ENABLE();
__HAL_RCC_GPIOH_CLK_ENABLE();
__HAL_RCC_GPIOA_CLK_ENABLE();
__HAL_RCC_GPIOB_CLK_ENABLE();
__HAL_RCC_GPIOG_CLK_ENABLE();
__HAL_RCC_GPIOE_CLK_ENABLE();
__HAL_RCC_GPIOD_CLK_ENABLE();

where unknown.

I added those missing interrupt definitions to a hfile in src, and all worked. That makes me think, that the include links do not work. Earlier I got some help by changing the include directory to 'Is a workspace path'.

I generated the same project (same definitions) to TrueStudio, and that worked, although also there were same kind of problems earlier with another try.

I cannot say, are these problems especially or only partly dependent on HAL, but life was easier before HAL.