It is recommended that you keep the repo/package name the same, but if you do change it, ensure you do a "Find all" using your IDE (or the built-in GitHub IDE by hitting the . key) and rename all instances of ros2_omni to whatever your project's name is.
Note that each directory currently has at least one file in it to ensure that git tracks the files (and, consequently, that a fresh clone has direcctories present for CMake to find). These example files can be removed if required (and the directories can be removed if CMakeLists.txt is adjusted accordingly).