I understood the solution. As it turned out, I was on the right track. Zend creates a hidden folder called .settings when creating the project.
For some reason, although it was included in the .gitignore file, it was deleted when switching between branches and resetting the database at a time.
I tried deleting the whole database and re-cloning earlier, but this did not work. The reason was that the .project file (also created by the Zend project file) was transferred to the repository, and upon repeated cloning, Zend saw this file and assumed that it was an existing project.
I also had to completely remove the .project file.
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