Passing a modified submodule to git annex --force-small triggers a failure:

cd "$(mktemp -d --tmpdir gx-XXXXXXX)"
git init
git annex init
git init sub
git -C sub commit --allow-empty -m"c0"
git submodule add ./sub

git -C sub commit --allow-empty -m"c1"
git commit -m'sub change'
git annex add --force-small sub

[...]
add sub (adding content to git repository) fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database
fatal: Unable to add (null) to database

git-annex: fd:18: hGetLine: end of file
failed
git-annex: user error (git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","hash-object","-w","--stdin-paths","--no-filters"] exited 128)

The demo above passes a submodule to annex add, but the more realistic scenario would be passing a directory (most likely ".") that happens to include a modified submodule.

The failure is happening when addSmallOverridden calls hash-object with the submodule path. As far as I can see, addSmallOverridden will only receive a directory if the path in question is a submodule (based on ls-files not traversing into submodules). So, perhaps an appropriate fix is to go through addFile rather hash-object/update-index when the file is a directory. I've included a patch to do that below. The first patch is for an issue in addSmallOverridden that I noticed when making the change.

From 58b5a1acf7dfe305b9284cf3423a58853c13451a Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Mon, 23 Mar 2020 15:45:15 -0400
Subject: [PATCH 1/2] add --force-small: Don't dereference link when checking
 file status

addSmallOverridden calls getFileStatus and then checks the result with
isSymbolicLink.  getFileStatus dereferences symbolic links, so
isSymbolicLink will always return false (assuming the getFileStatus
call doesn't fail on a broken link).  Use getSymbolicLinkStatus
instead.
---
 Command/Add.hs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Command/Add.hs b/Command/Add.hs
index e142aac0b..56e6fb236 100644
--- a/Command/Add.hs
+++ b/Command/Add.hs
@@ -107,7 +107,7 @@ addSmallOverridden :: RawFilePath -> Annex Bool
 addSmallOverridden file = do
    showNote "adding content to git repository"
    let file' = fromRawFilePath file
-  s <- liftIO $ getFileStatus file'
+  s <- liftIO $ getSymbolicLinkStatus file'
    if isSymbolicLink s
        then addFile file 
        else do
-- 
2.25.1

From c823d69a7b477f770fe539a74b788b61df173a76 Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Mon, 23 Mar 2020 15:45:15 -0400
Subject: [PATCH 2/2] add --force-small: Send all non-regular files through
 addFile

Running `git annex add --force-small` on a modified submodule fails
when the submodule path is fed to hash-object.  This failure is
unlikely to be triggered by a caller passing a submodule explicitly to
`git annex add` because there's nothing useful that annex-add can do
with a submodule.  A more likely scenario for hitting this failure is
that the caller passes "." or a subdirectory to `annex-add` while a
submodule underneath the specified path happens to be modified.

addSmallOverridden already routes symbolic links through addFile
rather than using the custom hash-object/update-index call.  The
latter is valid only for regular files, so extend this condition so
that everything that isn't a regular file goes through addFile.  Doing
so avoids the above error because submodules come in as directories.
---
 Command/Add.hs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Command/Add.hs b/Command/Add.hs
index 56e6fb236..72aae5f3c 100644
--- a/Command/Add.hs
+++ b/Command/Add.hs
@@ -108,7 +108,7 @@ addSmallOverridden file = do
    showNote "adding content to git repository"
    let file' = fromRawFilePath file
    s <- liftIO $ getSymbolicLinkStatus file'
-  if isSymbolicLink s
+  if not (isRegularFile s)
        then addFile file 
        else do
            -- Can't use addFile because the clean filter will
-- 
2.25.1

applied --Joey