I'm hoping to use git-annex in a project to manage large image files and maintain archived copies of them on removable USB drives. But I can't get this to work the way it's described in the walkthrough and in the "git-annex/tips/offline archive drives" example. Here's what I did:

    marshal@home[~]> git-annex version
    git-annex version: 5.20140412ubuntu1
    build flags: Assistant Webapp Webapp-secure Pairing Testsuite S3 WebDAV Inotify DBus DesktopNotify XMPP DNS Feeds Quvi TDFA CryptoHash
    key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SKEIN256E SKEIN512E SHA256 SHA1 SHA512 SHA224 SHA384 SKEIN256 SKEIN512 WORM URL
    remote types: git gcrypt S3 bup directory rsync web webdav tahoe glacier hook external

Create the local repo:

    marshal@home[~]> mkdir ~/annex
    marshal@home[~]> cd ~/annex
    marshal@home[~/annex]> git init
    Initialized empty Git repository in /home/marshal/annex/.git/
    marshal@home[~/annex]> git annex init "my laptop"
    init my laptop ok
    (Recording state in git...)

Create the remote repo (assume the warning can be ignored?)

    marshal@home[~/annex]> cd /media/marshal/Sony\ USB/
    marshal@home[/media/marshal/Sony USB]> git clone ~/annex
    Cloning into 'annex'...
    done.
    warning: remote HEAD refers to nonexistent ref, unable to checkout.
    marshal@home[/media/marshal/Sony USB]> cd annex
    marshal@home[/media/marshal/Sony USB/annex]> git annex init "usbdrive"
    init usbdrive ok
    (Recording state in git...)

Make them remotes of each other

    marshal@home[/media/marshal/Sony USB/annex]> git remote add laptop ~/annex
    marshal@home[/media/marshal/Sony USB/annex]> cd ~/annex
    marshal@home[~/annex]> git remote add usbdrive /media/marshal/Sony\ USB/annex/

Add some files into the local repo

    marshal@home[~/annex]> cp ~/Desktop/file* .
    marshal@home[~/annex]> git annex add .
    add file1.m3u ok
    add file2.sh ok
    add file3.pdf ok
    (Recording state in git...)
    marshal@home[~/annex]> git commit -a -m "added files"
    [master (root-commit) 4ea3be7] added files
     3 files changed, 3 insertions(+)
     create mode 120000 file1.m3u
     create mode 120000 file2.sh
     create mode 120000 file3.pdf

Change the preferred content settings

    marshal@home[~/annex]> git annex group usbdrive archive
    group usbdrive ok
    (Recording state in git...)
    marshal@home[~/annex]> git annex wanted usbdrive standard
    wanted usbdrive ok
    (Recording state in git...)

Sync to the usbdrive repo

    marshal@home[~/annex]> git annex sync usbdrive
    commit  ok
    pull usbdrive 
    remote: Counting objects: 7, done.
    remote: Compressing objects: 100% (3/3), done.
    remote: Total 5 (delta 1), reused 0 (delta 0)
    Unpacking objects: 100% (5/5), done.
    From /media/marshal/Sony USB/annex
     * [new branch]      git-annex  -> usbdrive/git-annex
    ok
    (merging usbdrive/git-annex into git-annex...)
    (Recording state in git...)
    push usbdrive 
    Counting objects: 29, done.
    Delta compression using up to 8 threads.
    Compressing objects: 100% (22/22), done.
    Writing objects: 100% (25/25), 2.44 KiB | 0 bytes/s, done.
    Total 25 (delta 3), reused 0 (delta 0)
    To /media/marshal/Sony USB/annex/
     * [new branch]      git-annex -> synced/git-annex
     * [new branch]      master -> synced/master
    ok

Copy eveything to the usbdrive repo

    marshal@home[~/annex]> git-annex copy --auto --to usbdrive
    copy file1.m3u (to usbdrive...) 
    SHA256E-s64061--c388e2c927cb4c88c11b1b5a8e166c4d8080dc528d53954dad1ee6d4933ce3c7.m3u
             64,061 100%   29.84MB/s    0:00:00 (xfr#1, to-chk=0/1)
    ok
    copy file2.sh (to usbdrive...) 
    SHA256E-s318--b8729560cc759d2256903feaa4ba65994ccbac94f30515d52a39083ad52e1bad.sh
                318 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=0/1)
    ok
    copy file3.pdf (to usbdrive...) 
    SHA256E-s32239--9b051067d5ef9f0cb4a01750901bf6bee3f9348e5b10138c8ef416ac8d51e5df.pdf
             32,239 100%    0.00kB/s    0:00:00 (xfr#1, to-chk=0/1)
    ok
    (Recording state in git...)

Check to see where git-annex "thinks" the files are

    marshal@home[~/annex]> git-annex whereis file1.m3u 
    whereis file1.m3u (2 copies) 
          	80fa5a68-3843-4e25-b4c9-53a8c51ba9ff -- here (my laptop)
           	d642b276-5f9b-4a5c-a42e-ea29cd9540b5 -- usbdrive
    ok

Check the filesystem results

    marshal@home[~/annex]> ls -la ~/annex
    total 48
    drwxrwxr-x  3 marshal marshal  4096 Jul 19 14:59 .
    drwxr-xr-x 99 marshal marshal 24576 Jul 19 14:55 ..
    lrwxrwxrwx  1 marshal marshal   194 Jul 19 14:59 file1.m3u -> .git/annex/objects/jq/MW/SHA256E-s64061--c388e2c927cb4c88c11b1b5a8e166c4d8080dc528d53954dad1ee6d4933ce3c7.m3u/SHA256E-s64061--c388e2c927cb4c88c11b1b5a8e166c4d8080dc528d53954dad1ee6d4933ce3c7.m3u
    lrwxrwxrwx  1 marshal marshal   188 Jul 19 14:59 file2.sh -> .git/annex/objects/1J/2K/SHA256E-s318--b8729560cc759d2256903feaa4ba65994ccbac94f30515d52a39083ad52e1bad.sh/SHA256E-    s318--b8729560cc759d2256903feaa4ba65994ccbac94f30515d52a39083ad52e1bad.sh
    lrwxrwxrwx  1 marshal marshal   194 Jul 19 14:59 file3.pdf -> .git/annex/objects/77/Wj/SHA256E-s32239--9b051067d5ef9f0cb4a01750901bf6bee3f9348e5b10138c8ef416ac8d51e5df.pdf/SHA256E-s32239--9b051067d5ef9f0cb4a01750901bf6bee3f9348e5b10138c8ef416ac8d51e5df.pdf
    drwxrwxr-x  9 marshal marshal  4096 Jul 19 15:04 .git
    marshal@home[~/annex]> ls -la /media/marshal/Sony\ USB/annex/
    total 4
    drwx------ 1 marshal marshal  144 Jul 19 14:56 .
    drwx------ 1 marshal marshal 4096 Jul 19 14:56 ..
    drwx------ 1 marshal marshal  448 Jul 19 14:57 .git

Why is there nothing in the usbdrive repo? And worse, why is the whereis command saying there are 2 copies?

But if I sync from the usbdrive repo, the files are copied

    marshal@home[~/annex]> cd /media/marshal/Sony\ USB/annex/
    marshal@home[/media/marshal/Sony USB/annex]> git-annex sync laptop
    (merging synced/git-annex origin/git-annex into git-annex...)
    (Recording state in git...)
    commit  ok
    pull laptop 
    remote: Counting objects: 23, done.
    remote: Compressing objects: 100% (8/8), done.
    remote: Total 11 (delta 3), reused 0 (delta 0)
    Unpacking objects: 100% (11/11), done.
    From /home/marshal/annex
     * [new branch]      git-annex  -> laptop/git-annex
     * [new branch]      master     -> laptop/master
     * [new branch]      synced/master -> laptop/synced/master
    
    
    Already up-to-date.
    ok
    (merging laptop/git-annex into git-annex...)
    (Recording state in git...)
    push laptop 
    Counting objects: 56, done.
    Delta compression using up to 8 threads.
    Compressing objects: 100% (24/24), done.
    Writing objects: 100% (33/33), 2.34 KiB | 0 bytes/s, done.
    Total 33 (delta 15), reused 0 (delta 0)
    To /home/marshal/annex
     * [new branch]      git-annex -> synced/git-annex
    ok
    marshal@home[/media/marshal/Sony USB/annex]> ls -la /media/marshal/Sony\ USB/annex/
    total 6
    drwx------ 1 marshal marshal  456 Jul 19 15:07 .
    drwx------ 1 marshal marshal 4096 Jul 19 14:56 ..
    lrwxrwxrwx 1 marshal marshal  396 Jul 19 15:07 file1.m3u -> .git/annex/objects/jq/MW/SHA256E-s64061--c388e2c927cb4c88c11b1b5a8e166c4d8080dc528d53954dad1ee6d4933ce3c7.m3u/SHA256E-s64061--c388e2c927cb4c88c11b1b5a8e166c4d8080dc528d53954dad1ee6d4933ce3c7.m3u
    lrwxrwxrwx 1 marshal marshal  384 Jul 19 15:07 file2.sh -> .git/annex/objects/1J/2K/SHA256E-s318--b8729560cc759d2256903feaa4ba65994ccbac94f30515d52a39083ad52e1bad.sh/SHA256E-s318--b8729560cc759d2256903feaa4ba65994ccbac94f30515d52a39083ad52e1bad.sh
    lrwxrwxrwx 1 marshal marshal  396 Jul 19 15:07 file3.pdf -> .git/annex/objects/77/Wj/SHA256E-s32239--9b051067d5ef9f0cb4a01750901bf6bee3f9348e5b10138c8ef416ac8d51e5df.pdf/SHA256E-s32239--9b051067d5ef9f0cb4a01750901bf6bee3f9348e5b10138c8ef416ac8d51e5df.pdf
    drwx------ 1 marshal marshal  448 Jul 19 15:07 .git

Why did I have to sync from the usbdrive? I expected the repo setup and the --auto option to copy the files. What am I missing?

Any help much appreciated.