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diff --git a/doc/bugs/Corrupted_.git__47__annex__47__index_when_running_assistant/comment_6_f0999dbd00e06ab2cbf68b58527c2b9b._comment b/doc/bugs/Corrupted_.git__47__annex__47__index_when_running_assistant/comment_6_f0999dbd00e06ab2cbf68b58527c2b9b._comment
new file mode 100644
index 000000000..f11e80bbe
--- /dev/null
+++ b/doc/bugs/Corrupted_.git__47__annex__47__index_when_running_assistant/comment_6_f0999dbd00e06ab2cbf68b58527c2b9b._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 6"""
+ date="2015-07-02T19:14:40Z"
+ content="""
+Yeah, --prune=now is bad news when using git-annex. At least, if
+you might be doing it at the same time that git-annex is staging
+objects in the index.
+
+Using it in combination with annex.alwayscommit=false is a particularly
+foot-shootish thing. I've added a warning to its documentation.
+
+`git gc` uses a lock file, `.git/gc.pid`. It might be possible for
+git-annex to hold that lock when it's in the process of staging and
+committing objects, to avoid `git gc` running at such times.
+"""]]
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
index 45b02ec66..a0d5a0b00 100644
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -862,6 +862,10 @@ Here are all the supported configuration settings.
   commit the data by running `git annex merge` (or by automatic merges)
   or `git annex sync`.
 
+  Note that you beware running `git gc` if using this configuration,
+  since it could garbage collect objects that are staged in git-annex's
+  index but not yet committed.
+
 * `annex.hardlink`
 
   Set this to `true` to make file contents be hard linked into the