git-annex/doc/bugs/git_annex_indirect_can_fail_catastrophically.mdwn

### Please describe the problem.

I have a repo that I initialized in direct mode because i felt unconfortable with the "symlink forest" approach.

Now that I prefer that, i want to switch back to indirect mode. The problem is, when I did that, I realized that some files in the repo were not writable by my user, and git annex indirect crashed, and didn't "indirect" all the files. Now the repo is in a "half-direct" state, and I seem to be unable to recover.

### What steps will reproduce the problem?

[[!format txt """
git init
git annex init
git annex direct
git annex add . # make sure some files are not writable by your user
git annex indirect
"""]]

The `indirect` step will stop at the file that is not writable and will fail to move some files to `.git/annex`. And then the repo is in `indirect` mode yet some files are still not symlinks.

Doing a `git annex direct` will try to commit all those nasty files into git, as it does a `git commit -a`.

### What version of git-annex are you using? On what operating system?

    git-annex version: 4.20130912-ga1faca3
    build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP DNS Feeds Quvi

Debian wheezy.

### Please provide any additional information below.

Ideally, there would be a way to just tell git annex it's really still in direct mode and migrate the remaining files.

The workaround is, obviously, to make sure you own all those files before messing around:

    chown -R you *
    chmod -R u+w *

A [[patch]], maybe, that allows you to flip cleanly between the two modes:

[[!format diff """
From a21dfc97da96883b2a088bb5f3f466296f08d858 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Antoine=20Beaupr=C3=A9?= <anarcat@koumbit.org>
Date: Mon, 16 Sep 2013 13:58:29 -0400
Subject: [PATCH] do not commit -a when going back to direct mode

without this, if we switched to indirect mode but failed doing so
(because of a permission problem, for example), going back to
direct mode will commit all files to git, which we really want 
to avoid.

---
 Command/Direct.hs |    1 -
 1 file changed, 1 deletion(-)

diff --git a/Command/Direct.hs b/Command/Direct.hs
index 7835988..ed8ea6c 100644
--- a/Command/Direct.hs
+++ b/Command/Direct.hs
@@ -33,7 +33,6 @@ perform = do
        showOutput
        _ <- inRepo $ Git.Command.runBool
                [ Param "commit"
-               , Param "-a"
                , Param "-m"
                , Param "commit before switching to direct mode"
                ]
--
1.7.10.4

"""]]

Any update on this? Why is `-a` used here? -- [[anarcat]]