Sean Hammond wrote:
> 1. The total number of files in ~/Annex, not including .git, on A
> and B is different:
> 
> ls -R1 ~/Annex | wc -l
> 21830
> 
> ls -R1 ~/Annex | wc -l
> 21845
> 
> 2. git-annex status shows untracked and modified files on both
> machines (different files on each machine).

These seem likely to be related. Can you show the status?

Are you using direct mode, or indirect mode?

> 3. On each machine, 7 files have been replaced with broken symlinks
> to files in .git/objects. This time it is the same files on both
> machines, so it looks as if git-annex might have lost these files
> from both machines. git-annex fsck finds these 7 and reports them as
> 'No known copies exist'.

You run git annex log on some of these files to see the history of which
repository they were in and how they moved around.

For example:

- 2013-11-27 10:01:14 Parallel_and_Concurrent_Programming_in_Haskell.epub | 
d322dff8-8b32-11e0-bbce-bb98bc1ede5b -- wren
+ 2013-11-25 17:40:59 Parallel_and_Concurrent_Programming_in_Haskell.epub | 
7e88d964-437e-47be-885a-e158af656729 -- darkstar
+ 2013-11-25 17:13:34 Parallel_and_Concurrent_Programming_in_Haskell.epub | 
d322dff8-8b32-11e0-bbce-bb98bc1ede5b -- wren
+ 2013-11-25 17:13:34 Parallel_and_Concurrent_Programming_in_Haskell.epub | 
00000000-0000-0000-0000-000000000001 -- web

So, this would also let you see where the last copy resided, and when it was
recorded as being dropped. Although git-annex should never drop the last copy
of a file on its own in normal circumstances.

> 4. Even after running git gc --aggressive --prune and git-annex
> dropunused, the .git directories are massive: 23G and 2.5G, for just
> ~20,000 files.

Are you looking at the sizes of the .git/objects directories, or the
.git/annex/objects directories? (.git/annex/tmp is also a possible place where
cruft could somehow accumulate)

When you ran git annex dropunused, did it drop something? git annex unused
should not find any unused files if you've just synced 2 directories, and never
deleted any of the files yet.

-- 
see shy jo

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