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By default, TeamCity displays projects, their subprojects, build configurations and templates in the alphabetical order.
Starting from TeamCity 9.1, project administrators can apply custom ordering to subprojects and build configurations on the Project Settings page for the parent project and use it as the default order.

To enable reordering, use the corresponding button above the list.

Individual users can still manually tweak the display using the up-down button in the Configure Visible Projects pop-up on the Projects Overview page.