Nested git repositories without remotes (a.k.a. git submodule without remotes)

Chris's answer don't assume for a "master" repo (master being the default name of the main branch in Git, not a repo).

It declares submodules in a "parent" repo, which in your case would be "main".

So you need three independent repo "one" "two" and "three" setup elsewhere, and then clone and add them to your "main" repo as submodules:

# first remove the one directory previously added
git rm --cached one
# then declare the external one repo as a submodule in "main" repo)
git submodule add /path/to/one.git one

You can do what you want, but your one, two, and three would need to be accessible to whoever will need to clone them—this is not usually the case for “random” development repositories.

If you do set this up, you will need to be very careful not to delete “your” repository (or make it otherwise inaccessible) since it is not just “yours”: it will be origin in your collaborator’s clones and it will serve as the “central”/“upstream” repository (as specified in .gitmodules).

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If all your collaborators are local (and can read from the repositories), you can add your existing sub-repositories as submodules by giving their local paths as URLs:

git rm --cached one two three
git submodule add `pwd`/one
git submodule add `pwd`/two
git submodule add `pwd`/three

If not all your collaborators will be working on the same machine, then that will probably not work correctly (since it will store a local path in .gitmodules; non-local collaborators would have to adjust the URLs after git submodule init).

If your one, two, and three are remotely Git-accessible, then you can specify their effecive URLs instead:

git rm --cached one two three
git submodule add server:/path/to/your/main/one
git submodule add server:/path/to/your/main/two
git submodule add server:/path/to/your/main/three

In both cases, since you already have a sub-repository in place, git submodule add will use that instead of trying to clone from the specified path/URL.