update documentation that mentioned .git-annex/

doc/bare_repositories.mdwn

@@ -17,10 +17,6 @@ Known to work ok:
 
 There are a few caveats to keep in mind when using bare repositories:
 
-* `git annex init` can be run in a bare repository, but it cannot
-  store the name you gave the repository in .git-annex/uuid.log (because
-  the bare repository has no such file to commit to). Instead, it will
-  tell you a command to run in some non-bare clone of the repository.
 * Some subcommands, like `fsck`, `trust`, `unused` and `fromkey`, 
   cannot be run in a bare repository. Those subcommands will
   refuse to do anything.

doc/design/encryption.mdwn

@@ -36,7 +36,7 @@ There does not seem to be much benefit to using the same cipher for
 two different encrypted remotes.
 
 So, the encrypted cipher could just be stored with the rest of a remote's
-configuration in `.git-annex/remotes.log` (see [[internals]]). When `git
+configuration in `remotes.log` (see [[internals]]). When `git
 annex intiremote` makes a remote, it can generate a random symmetric
 cipher, and encrypt it with the specified gpg key. To allow another gpg
 public key access, update the encrypted cipher to be encrypted to both gpg

doc/git-annex.mdwn

@@ -497,18 +497,6 @@ These files are used by git-annex, in your git repository:
 `.git/annex/objects/` contains the annexed file contents that are currently
 available. Annexed files in your git repository symlink to that content.
 
-`.git-annex/uuid.log` is used to map between repository UUID and
-descriptions.
-
-`.git-annex/trust.log` is used to indicate which repositories are trusted
-and untrusted.
-
-`.git-annex/*.log` is where git-annex records its content tracking
-information. These files should be committed to git.
-
-`.gitattributes` is configured to use git's union merge driver
-to avoid conflicts when merging files in the `.git-annex` directory.
-
 # SEE ALSO
 
 Most of git-annex's documentation is available on its web site, 

doc/internals.mdwn

@@ -17,7 +17,15 @@ This two-level structure is used because it allows the write bit to be removed
 from the subdirectories as well as from the files. That prevents accidentially
 deleting or changing the file contents.
 
-## `.git-annex/uuid.log`
+## The git-annex branch
+
+This branch is managed by git-annex, with the contents listed below.
+
+Note that it assumes only it will modify the branch. If you go in and make
+changes, be sure to remove `.git/index.git-annex` before running git-annex,
+otherwise it will probably revert your changes in its next commit to the branch.
+
+### `uuid.log`
 
 Records the UUIDs of known repositories, and associates them with a
 description of the repository. This allows git-annex to display something
@@ -30,7 +38,7 @@ space and then the description through to the end of the line. Example:
 	e605dca6-446a-11e0-8b2a-002170d25c55 laptop
 	26339d22-446b-11e0-9101-002170d25c55 usb disk
 
-## `git-annex/remotes.log`
+## `remotes.log`
 
 Holds persistent configuration settings for [[special_remotes]] such as
 Amazon S3.
@@ -39,7 +47,7 @@ The file format is one line per remote, starting with the uuid of the
 remote, followed by a space, and then a series of key=value pairs,
 each separated by whitespace.
 
-## `.git-annex/trust.log`
+## `trust.log`
 
 Records the [[trust]] information for repositories. Does not exist unless
 [[trust]] values are configured.
@@ -53,7 +61,7 @@ Example:
 	e605dca6-446a-11e0-8b2a-002170d25c55 1
 	26339d22-446b-11e0-9101-002170d25c55 ?
 
-## `.git-annex/aaa/bbb/*.log`
+## `aaa/bbb/*.log`
 
 The remainder of the log files record [[location_tracking]] information
 for file contents. Again these are placed in two levels of subdirectories

doc/location_tracking.mdwn

@@ -1,5 +1,5 @@
 git-annex keeps track of in which repositories it last saw a file's content.
-This location tracking information is stored in `.git-annex/$key.log`.
+This location tracking information is stored in the git-annex branch.
 Repositories record their UUID and the date when they get or drop 
 a file's content. (Git is configured to use a union merge for this file,
 so the lines may be in arbitrary order, but it will never conflict.)

doc/walkthrough/modifying_annexed_files.mdwn

@@ -26,8 +26,7 @@ and this symlink is what gets committed to git in the end.
 	# git commit my_cool_big_file -m "changed an annexed file"
 	add my_cool_big_file ok
 	[master 64cda67] changed an annexed file
-	 2 files changed, 2 insertions(+), 1 deletions(-)
-	 create mode 100644 .git-annex/WORM-s30-m1289672605--file.log
+	 1 files changed, 1 insertions(+), 1 deletions(-)
 
 There is one problem with using `git commit` like this: Git wants to first
 stage the entire contents of the file in its index. That can be slow for