Example - on http://datasets.datalad.org we have a few hundred datasets organized into a hierarchy as git submodules. Each git submodules carries its own .git/ directory so they are "self sufficient" and we could readily assess their sizes, and "cut the tree" at any level without looking for the supermodule somewhere high up in the tree. .gitmodules typically has relative paths for the url and path for the submodules there, the form which I think we chose because it used to work (I could be utterly wrong! but I think it was done in an informed fashion) for git clone --recursive: $> curl http://datasets.datalad.org/labs/gobbini/famface/.gitmodules [submodule "data"] path = data url = ./data and possibly outside: $> curl http://datasets.datalad.org/labs/gobbini/famface/data/.gitmodules [submodule "scripts/mridefacer"] path = scripts/mridefacer url = https://github.com/yarikoptic/mridefacer But unfortunately git doesn't even consider such (valid AFAIK) situation while cloning where url has to have .git suffix but repository is not bare and a relative "data" path (or "./data" url) is referring to the worktree. $> git clone --recursive http://datasets.datalad.org/labs/gobbini/famface/.git Cloning into 'famface'... remote: Counting objects: 61, done. remote: Compressing objects: 100% (54/54), done. remote: Total 61 (delta 14), reused 0 (delta 0) Unpacking objects: 100% (61/61), done. Submodule 'data' (http://datasets.datalad.org/labs/gobbini/famface/.git/data) registered for path 'data' Cloning into '/tmp/famface/data'... fatal: repository 'http://datasets.datalad.org/labs/gobbini/famface/.git/data/' not found fatal: clone of 'http://datasets.datalad.org/labs/gobbini/famface/.git/data' into submodule path '/tmp/famface/data' failed Failed to clone 'data'. Retry scheduled Cloning into '/tmp/famface/data'... fatal: repository 'http://datasets.datalad.org/labs/gobbini/famface/.git/data/' not found fatal: clone of 'http://datasets.datalad.org/labs/gobbini/famface/.git/data' into submodule path '/tmp/famface/data' failed Failed to clone 'data' a second time, aborting on the server I use the "smart HTTP" git backend, but not sure if that is the one to blame, since I do not see in the logs any attempt to get the /data from not under .git/: 10.31.188.88 - - [13/Dec/2018:12:18:38 -0500] "GET /labs/gobbini/famface/.git/info/refs?service=git-upload-pack HTTP/1.1" 200 681 "-" "git/2.20.0.rc2.403.gdbc3b29805" 10.31.188.88 - - [13/Dec/2018:12:18:38 -0500] "POST /labs/gobbini/famface/.git/git-upload-pack HTTP/1.1" 200 69276 "-" "git/2.20.0.rc2.403.gdbc3b29805" ==> datasets.datalad.org-error.log <== [Thu Dec 13 12:18:38.673447 2018] [core:info] [pid 7570:tid 140683541153536] [client 10.31.188.88:32794] AH00128: File does not exist: /srv/datasets.datalad.org/www/labs/gobbini/famface/.git/data/info/refs ==> datasets.datalad.org-access-comb.log <== 10.31.188.88 - - [13/Dec/2018:12:18:38 -0500] "GET /labs/gobbini/famface/.git/data/info/refs?service=git-upload-pack HTTP/1.1" 404 485 "-" "git/2.20.0.rc2.403.gdbc3b29805" ==> datasets.datalad.org-error.log <== [Thu Dec 13 12:18:38.689277 2018] [core:info] [pid 7572:tid 140683574724352] [client 10.31.188.88:32796] AH00128: File does not exist: /srv/datasets.datalad.org/www/labs/gobbini/famface/.git/data/info/refs ==> datasets.datalad.org-access-comb.log <== 10.31.188.88 - - [13/Dec/2018:12:18:38 -0500] "GET /labs/gobbini/famface/.git/data/info/refs?service=git-upload-pack HTTP/1.1" 404 485 "-" "git/2.20.0.rc2.403.gdbc3b29805" -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik