Holoped,
You are quite correct, there is an interface issue with any electronics scheme which connects the Pi directly to the A4988.
The schematic indicates that the driver is connected to +5V, yet the Raspberry pi GPIO are 3.3V logic level outputs. The datasheet for the driver confirms that the logic HIGH must be >0.7*5V that is >3.5V. The driver logic supply must either be connected to 3.3V or level translators used to make the interface compatible. The former is acceptable since the A4988 is specified to work at 3.3V. Failure to adopt either approach may result in erratic or non-operation, depending upon device and supply tolerances, temperature or amount of noise on supply. Quite a few people have reported issues with erratic stepper operation; this is probably the reason. My own experience confirms this.
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