git-annex-shell: Added support for operating inside gcrypt repositories.

* Note that the layout of gcrypt repositories has changed, and
  if you created one you must manually upgrade it.
  See http://git-annex.branchable.com/upgrades/gcrypt/

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+Unfortunately the initial gcrypt repository layout had to be changed
+after git-annex version 4.20130920. If you have an encrypted git repository
+created using version 4.20130920 or 4.20130909, you need to manually
+upgrade it.
+
+If you look at the contents of your gcrypt repository, you will
+see a bare git repository, with a few three-letter subdirectories,
+which are where git-annex stores its encrypted file contents:
+
+<pre>
+27f/  branches/  description  hooks/  objects/
+HEAD  config     f37/         info/   refs/
+</pre>
+
+In the example above, the subdirectories are `27f` and `f37`.
+
+All you need to do to transition is move those subdirectories
+into an `annex/objects` directory.
+
+	mkdir annex ; mkdir annex/objects ; mv 27f f37 annex/objects
+
+Probably those are the only 3 letter things inside your git repository,
+so this will probably work:
+
+	mkdir annex ; mkdir annex/objects ; mv ??? annex