I understand how to use git submodule to reference a specific commit in another repo, but where is that reference actually stored? It doesn't seem to be in .gitmodules as plain text?

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The .gitmodules file just records the path and remote URL to the submodule repository. The commit itself is stored in the tree object. You can query it like this:

git ls-tree <ref> <path>

where <ref> is a reference to some commit (e.g. HEAD, master, a commit SHA sum) and <path> is a path to a submodule.

The output looks something like this:

160000 commit <sha> <path>

where <sha> is the commit in the submodule. The number in front has the following meaning, according to the Git book:

Notice the 160000 mode for the DbConnector (submodule path of the example used in the book) entry. That is a special mode in Git that basically means you’re recording a commit as a directory entry rather than a subdirectory or a file.

See also this question on StackOverflow.

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