Documentation: do not mention .git/refs/* directories

It is an implementation detail that a new tag is created by adding a
file in the .git/refs/tags directory.  The only thing the user needs
to know is that a "git tag" creates a ref in the refs/tags namespace,
and without "-f", it does not overwrite an existing tag.

Inspired by a report from 乙酸鋰 <ch3cooli@gmail.com>; I think I
caught all the existing mention in Documentation/ directory in the
tip of 1.7.9.X maintenance track, but we may have added new ones
since then.

Signed-off-by: Junio C Hamano <gitster@pobox.com>

Documentation/git-describe.txt

@@ -36,12 +36,12 @@ OPTIONS
 
 --all::
 	Instead of using only the annotated tags, use any ref
-	found in `.git/refs/`.  This option enables matching
+	found in `refs/` namespace.  This option enables matching
 	any known branch, remote-tracking branch, or lightweight tag.
 
 --tags::
 	Instead of using only the annotated tags, use any tag
-	found in `.git/refs/tags`.  This option enables matching
+	found in `refs/tags` namespace.  This option enables matching
 	a lightweight (non-annotated) tag.
 
 --contains::

Documentation/git-filter-branch.txt

@@ -32,7 +32,8 @@ changes, which would normally have no effect.  Nevertheless, this may be
 useful in the future for compensating for some git bugs or such,
 therefore such a usage is permitted.
 
-*NOTE*: This command honors `.git/info/grafts` and `.git/refs/replace/`.
+*NOTE*: This command honors `.git/info/grafts` file and refs in
+the `refs/replace/` namespace.
 If you have any grafts or replacement refs defined, running this command
 will make them permanent.
 

Documentation/git-fsck.txt

@@ -23,8 +23,8 @@ OPTIONS
 	An object to treat as the head of an unreachability trace.
 +
 If no objects are given, 'git fsck' defaults to using the
-index file, all SHA1 references in .git/refs/*, and all reflogs (unless
---no-reflogs is given) as heads.
+index file, all SHA1 references in `refs` namespace, and all reflogs
+(unless --no-reflogs is given) as heads.
 
 --unreachable::
 	Print out objects that exist but that aren't reachable from any

Documentation/git-lost-found.txt

@@ -48,7 +48,8 @@ $ gitk $(cd .git/lost-found/commit && echo ??*)
 ------------
 
 After making sure you know which the object is the tag you are looking
-for, you can reconnect it to your regular .git/refs hierarchy.
+for, you can reconnect it to your regular `refs` hierarchy by using
+the `update-ref` command.
 
 ------------
 $ git cat-file -t 1ef2b196

Documentation/git-pack-refs.txt

@@ -14,21 +14,23 @@ DESCRIPTION
 -----------
 
 Traditionally, tips of branches and tags (collectively known as
-'refs') were stored one file per ref under `$GIT_DIR/refs`
+'refs') were stored one file per ref in a (sub)directory
+under `$GIT_DIR/refs`
 directory.  While many branch tips tend to be updated often,
 most tags and some branch tips are never updated.  When a
 repository has hundreds or thousands of tags, this
 one-file-per-ref format both wastes storage and hurts
 performance.
 
 This command is used to solve the storage and performance
-problem by stashing the refs in a single file,
+problem by storing the refs in a single file,
 `$GIT_DIR/packed-refs`.  When a ref is missing from the
-traditional `$GIT_DIR/refs` hierarchy, it is looked up in this
+traditional `$GIT_DIR/refs` directory hierarchy, it is looked
+up in this
 file and used if found.
 
 Subsequent updates to branches always create new files under
-`$GIT_DIR/refs` hierarchy.
+`$GIT_DIR/refs` directory hierarchy.
 
 A recommended practice to deal with a repository with too many
 refs is to pack its refs with `--all --prune` once, and
@@ -57,6 +59,15 @@ a repository with many branches of historical interests.
 The command usually removes loose refs under `$GIT_DIR/refs`
 hierarchy after packing them.  This option tells it not to.
 
+
+BUGS
+----
+
+Older documentation written before the packed-refs mechanism was
+introduced may still say things like ".git/refs/heads/<branch> file
+exists" when it means "branch <branch> exists".
+
+
 GIT
 ---
 Part of the linkgit:git[1] suite

Documentation/git-replace.txt

@@ -14,14 +14,13 @@ SYNOPSIS
 
 DESCRIPTION
 -----------
-Adds a 'replace' reference in `.git/refs/replace/`
+Adds a 'replace' reference in `refs/replace/` namespace.
 
 The name of the 'replace' reference is the SHA1 of the object that is
 replaced. The content of the 'replace' reference is the SHA1 of the
 replacement object.
 
-Unless `-f` is given, the 'replace' reference must not yet exist in
-`.git/refs/replace/` directory.
+Unless `-f` is given, the 'replace' reference must not yet exist.
 
 Replacement references will be used by default by all git commands
 except those doing reachability traversal (prune, pack transfer and

Documentation/git-tag.txt

@@ -18,11 +18,10 @@ SYNOPSIS
 DESCRIPTION
 -----------
 
-Add a tag reference in `.git/refs/tags/`, unless `-d/-l/-v` is given
+Add a tag reference in `refs/tags/`, unless `-d/-l/-v` is given
 to delete, list or verify tags.
 
-Unless `-f` is given, the tag to be created must not yet exist in the
-`.git/refs/tags/` directory.
+Unless `-f` is given, the named tag must not yet exist.
 
 If one of `-a`, `-s`, or `-u <key-id>` is passed, the command
 creates a 'tag' object, and requires a tag message.  Unless