diff --git a/Command/Smudge.hs b/Command/Smudge.hs
index 6718b4908a..1e169c1bf1 100644
--- a/Command/Smudge.hs
+++ b/Command/Smudge.hs
@@ -8,6 +8,7 @@
 module Command.Smudge where
 
 import Command
+import qualified Annex
 import Annex.Content
 import Annex.Link
 import Annex.FileMatcher
@@ -54,6 +55,8 @@ smudge file = do
 			ifM (inAnnex k)
 				( do
 					content <- calcRepo (gitAnnexLocation k)
+					whenM (annexThin <$> Annex.getGitConfig) $
+						warning $ "Not able to honor annex.thin when git is checking out " ++ file ++ " (run git annex fix to re-thin files)"
 					liftIO $ B.putStr . fromMaybe b
 						=<< catchMaybeIO (B.readFile content)
 				, liftIO $ B.putStr b
diff --git a/debian/changelog b/debian/changelog
index 05ee3dbd31..6a486b4bf5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+git-annex (6.20160413) UNRELEASED; urgency=medium
+
+  * smudge: Print a warning when annex.thin is set, as git's smudge
+    interface does not allow honoring that configuration.
+
+ -- Joey Hess <id@joeyh.name>  Wed, 13 Apr 2016 13:30:32 -0400
+
 git-annex (6.20160412) unstable; urgency=medium
 
   * adjust --unlock: Enters an adjusted branch in which all annexed files
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
index 65b5dc7010..b9d9221fda 100644
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -932,8 +932,8 @@ Here are all the supported configuration settings.
   Set this to `true` to make unlocked files be a hard link to their content
   in the annex, rather than a second copy. (Only when supported by the file
   system, and only in repository version 6.) This can save considerable
-  disk space, but modification made to a file will lose the local (and
-  possibly only) copy of the old version. So, enable with care.
+  disk space, but when a modification is made to a file, you will lose the
+  local (and possibly only) copy of the old version. So, enable with care.
 
   After setting (or unsetting) this, you should run `git annex fix` to
   fix up the annexed files in the work tree to be hard links (or copies).
diff --git a/doc/tips/unlocked_files.mdwn b/doc/tips/unlocked_files.mdwn
index 20605b6122..3a74043f04 100644
--- a/doc/tips/unlocked_files.mdwn
+++ b/doc/tips/unlocked_files.mdwn
@@ -135,6 +135,11 @@ make the second copy not be worth keeping:
 In situations like these, you may want to avoid the overhead of the second
 local copy of unlocked files. There's a config setting for that.
 
+[[!template id=note text="""
+Note that setting annex.thin only has any effect on systems that support
+hard links. It is supported on Windows, but not on FAT filesystems.
+"""]]
+
 	git config annex.thin true
 
 After changing annex.thin, you'll want to fix up the work tree to
@@ -142,8 +147,12 @@ match the new setting:
 
 	git annex fix
 
-Note that setting annex.thin only has any effect on systems that support
-hard links. It is supported on Windows, but not on FAT filesystems.
+Unfortunately, git's smudge interface does not let git-annex honor
+the annex.thin configuration when git is checking out a file.
+So, using `git checkout` to check out a different branch, or even 
+`git merge` can result in some non-thin files making their way into the
+working tree, and using more disk space. A warning will be printed out in
+this situation. You can always run `git annex fix` to re-thin such files.
 
 ## tradeoffs