Submodule deletion not synced from adjusted branch

This is conceptually a continuation of a previous issue: https://git-annex.branchable.com/bugs/Sync_of_adjusted_branch_does_not_propagate_changed_submodule_commit/

That was about git annex sync propagating submodule modifications back to the main branch. When looking into debugging a DataLad test failure involving adjusted branches, I realized that there is still an issue with submodule deletions not being propagated back.

Here's a demo:

set -eu

cd "$(mktemp -d "${TMPDIR:-/tmp}"/ga-sync-sub-del-XXXX)"

git init
git commit -mc0 --allow-empty
git init sub
git -C sub commit -m'c0 sub' --allow-empty
git submodule add --name sub ./sub
git commit -m'add sub'

git annex init
git annex adjust --unlock

git rm sub
git commit -m'remove sub'
git annex sync

git log --format="* %s %d" -p -2

With a git-annex built from 8.20201129-72-gf35469764, the submodule deletion remains on the adjusted branch:

[...]
* git-annex adjusted branch  (HEAD -> adjusted/master(unlocked))

diff --git a/sub b/sub
deleted file mode 160000
index 95031de..0000000
--- a/sub
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 95031de9306714e09dc535246ef77b9e155999be
* remove sub  (synced/master, master, refs/basis/adjusted/master(unlocked))

diff --git a/.gitmodules b/.gitmodules
index c489803..e69de29 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "sub"]
-   path = sub
-   url = ./sub

I tried my hand at fixing this with the attached patch. I'm not confident that it's the right fix, but with it the output of the above demo looks as I'd expect (and the git-annex tests still pass):

[...]
* git-annex adjusted branch  (HEAD -> adjusted/master(unlocked))
* remove sub  (synced/master, master, refs/basis/adjusted/master(unlocked))

diff --git a/.gitmodules b/.gitmodules
index c489803..e69de29 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "sub"]
-   path = sub
-   url = ./sub
diff --git a/sub b/sub
deleted file mode 160000
index 102197a..0000000
--- a/sub
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 102197a8b5692dc07dde7c1f6dd2f51c7ec6834e

Thanks for taking a look.

From e7abf01499fbd5593044889da529834e1b2999bc Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Wed, 6 Jan 2021 19:16:30 -0500
Subject: [PATCH] adjustTree: Consider submodule deletions

In addition to regular file deletions, the removefiles argument passed
to adjustTree may contain removed submodules.  When making the new
tree, filter these out in the same way that is done for regular files
so that the deletion is propagated.
---
 Git/Tree.hs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Git/Tree.hs b/Git/Tree.hs
index 491314fff..d5ac59ea7 100644
--- a/Git/Tree.hs
+++ b/Git/Tree.hs
@@ -259,6 +259,7 @@ adjustTree adjusttreeitem addtreeitems resolveaddconflict removefiles r repo =
 
    removeset = S.fromList $ map (normalise . gitPath) removefiles
    removed (TreeBlob f _ _) = S.member (normalise (gitPath f)) removeset
+  removed (TreeCommit f _ _) = S.member (normalise (gitPath f)) removeset
    removed _ = False
 
    addoldnew [] new = new

base-commit: f3546976483aa4c29e1050081af6d5a03290e25b
-- 
2.30.0.284.gd98b1dd5ea

done thanks! --Joey