So I know about git submodules and subtrees. But I also used to be able to have nested full Git repositories treated as nothing simple filesystem subdirectories?
For example, given:
topdir/
    file1
    file2
    subdir1/
        file1
        file2
    subdir2/
        file1
        file2
    subdir3/
        .git/
        file1
        file2
Previously, simply executing:
$ git init && git commit -a .
in topdir would result in the files of subdir3 being committed as a raw or literal subdirectory (i.e. not a submodule), with the '.git' directory in the subdirectory ignored in the super- or top-level repository. Entering subdir3 would make subdir3/.git to current repository. 
With 1.8.2.1.501, there does not seem to be any way to get this behavior back. Running the above command now results in subdir3 being considered a submodule but, perversely not added to the index. I have to explicitly do a git submodule add to add the files under it to the main repo.
When did this change happen?
Is there any way to get the old behavior back, i.e., have the subdirectory treated as a regular directory, and not a git submodule or subtree?