Arduino for STM32

This is another good resource for LCD displays with I2C backpacks: https://arduinoinfo.mywikis.net/wiki/LCD-Blue-I2C

My suggestion is that you try to get away from the prototype cables and weld everything with wires as short as possible on a perforated plate. Join strand by strand carefully, the arrangement you have it should work smoothly
An old fashioned wire-wrap tool makes a much better connection that ...

I just ran a test,

To use USB serial, turn switch #3 off and press reset.

Under Linux:
[389728.082943] usb 5-1: Product: BLACKPILL_F401CC CDC in FS Mode
[389728.082946] usb 5-1: Manufacturer: STMicroelectronics
[389728.082949] usb 5-1: SerialNumber: 356436553433
[389728.116170] cdc_acm 5-1:1.0 ...

I have a few of those boards.

For development, I keep switch #3 on and the others off.

Pressing reset enables DFU mode and enables uploading a program.

SerialUSB works without any issues. Enable Serial in the CDC options.

To upload again, press reset to enable DFU mode.

To see the pins ...

ST-Link on Linux does not have a port assigned:
[93510.859888] usb 5-2: new full-speed USB device number 2 using uhci_hcd
[93511.033906] usb 5-2: New USB device found, idVendor=0483, idProduct=3748, bcdDevice= 1.00
[93511.033914] usb 5-2: New USB device strings: Mfr=1, Product=2, SerialNumber=3 ...

Official STM32 v2.0 core with STM32Cube programmer makes this process easy.
Sketch uses 10316 bytes (1%) of program storage space. Maximum is 524288 bytes.
Global variables use 620 bytes (0%) of dynamic memory, leaving 130452 bytes for local variables. Maximum is 131072 bytes ...

What situation do you use the "CDC (no generic serial)" ?

No generic serial on both the CDC and USART is my normal setting.
This way, you are free to rename the serial ports to your liking.

Here is a GPS example adapted from one of mburnette's projects:
#define console SerialUSB
// GPS module ...

In my experience, with the non-Maple Mini boards, you have 2 viable options: ST-Link and using the internal serial firmware loader. The bootloader is just a nuisance.

I agree: viewtopic.php?p=6984#p6984

Secondly, If i managed how to do this, which library for SPI flash(W25Q64) should I use? Does it matter?
The W25Q64 has a thorough data sheet showing the commands.

I found a library for a W25Q16 at https://github.com/derekevans/W25Q16 . The commands in this library match the W25Q64 data sheet, so ...

You may want to consider refactoring the code to use arrays of binary values instead of booleans.
I would expect this to be much more efficient, as the arrays are simplified from two dimensions to one.
const uint32_t outmuxChannel[] =
{
0B0011111111110000, //channel 0
0B0011111111111000 ...