gitmodules file at the root of the source tree assigns a logical name to the submodule and describes the default URL the submodule shall be cloned from. Submodules are composed from a so-called gitlink tree entry in the main repository that refers to a particular commit object within the inner repository that is completely separate. Directories that come from both projects can be cloned and checked out as a whole if you choose to go that route. If you want to merge the project histories and want to treat the aggregated whole as a single project from then on, you may want to add a remote for the other project and use the subtree merge strategy, instead of treating the other project as a submodule. They are not to be confused with remotes, which are meant mainly for branches of the same project submodules are meant for different projects you would like to make part of your source tree, while the history of the two projects still stays completely independent and you cannot modify the contents of the submodule from within the main project. Submodules allow foreign repositories to be embedded within a dedicated subdirectory of the source tree, always pointed at a particular commit.
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