How do I init submodules nested in a subtree?

Question

Apparently, adding a subtree of a repository that has submodules will break git submodule init. Here is a script which reproduces the problem:

#!/bin/sh
set -ex

mkdir submod
cd submod
git init
touch foo
git add foo
git commit -asm "This is a submodule"
cd ..

mkdir subtree
cd subtree
git init
git submodule add `realpath ../submod` submod
git commit -asm "This has reference to submodule"
cd ..

mkdir top
cd top
git init
touch bar
git add bar
git commit -asm "Dummy commit so HEAD resolves correctly"
git subtree add --prefix=subtree `realpath ../subtree` master

# This fails!
git submodule init

What this script is doing is:

1. Create a repo submod
2. Create a repo subtree that has a submodule reference to submod
3. Create a repo top that has a subtree reference to subtree

Upon further consideration, it is clear what the problem is: the subtree mechanism has added subtree's submodule reference to submod to the tree, but the .gitmodules metadata remains in subtree/.gitmodules, not the top-level .gitmodules, which means that git submodule init fails. If we copy the contents of subtree/.gitmodules to .gitmodules, adjusting all the paths accordingly, that solves the problem...

[submodule "submod"]
    path = subtree/submod
    url = /Users/ezyang/Dev/labs/git-subtree-submod/submod

...but it is a bit of pain if the subtree has a lot of submodules. Is there a better way to do this?

Answer 1

From what I can tell reading the docs and source code... Git subtree is completely separate from Git submodules and will not actively manage any submodules that may be contained within the subtree project itself.

As you found out, .gitmodules, which is critical to the function of git submodule init, needs to be maintained in the root of the "main" repository (for lack of a better term).

Upon further consideration, it is clear what the problem is: the subtree mechanism has added subtree's submodule reference to submod to the tree, but the .gitmodules metadata remains in subtree/.gitmodules, not the top-level .gitmodules, which means that git submodule init fails. If we copy the contents of subtree/.gitmodules to .gitmodules, adjusting all the paths accordingly, that solves the problem...

I strongly recommend not mixing these features.