Update README to reflect the hierarchical tree objects,

and other newfangled things like merging.

Also, talk more about the actual operations, and give some
rough examples of what you can do.

1 files changed, 401 insertions, 109 deletions

diff --git a/README b/README
index cf550e258c..d4fa56f7c6 100644
--- a/README
+++ b/README
@@ -1,6 +1,9 @@
 
+
+
 	GIT - the stupid content tracker
 
+
 "git" can mean anything, depending on your mood.
 
  - random three-letter combination that is pronounceable, and not
@@ -17,127 +20,196 @@ doesn't do a whole lot, but what it _does_ do is track directory
 contents efficiently. 
 
 There are two object abstractions: the "object database", and the
-"current directory cache".
+"current directory cache" aka "index".
+
+
 
 	The Object Database (SHA1_FILE_DIRECTORY)
 
+
 The object database is literally just a content-addressable collection
 of objects.  All objects are named by their content, which is
 approximated by the SHA1 hash of the object itself.  Objects may refer
 to other objects (by referencing their SHA1 hash), and so you can build
 up a hierarchy of objects. 
 
-There are several kinds of objects in the content-addressable collection
-database.  They are all in deflated with zlib, and start off with a tag
-of their type, and size information about the data.  The SHA1 hash is
-always the hash of the _compressed_ object, not the original one.
-
-In particular, the consistency of an object can always be tested
+All objects have a statically determined "type" aka "tag", which is
+determined at object creation time, and which identifies the format of
+the object (ie how it is used, and how it can refer to other objects). 
+There are currently three different object types: "blob", "tree" and
+"commit". 
+
+A "blob" object cannot refer to any other object, and is, like the tag
+implies, a pure storage object containing some user data.  It is used to
+actually store the file data, ie a blob object is associated with some
+particular version of some file. 
+
+A "tree" object is an object that ties one or more "blob" objects into a
+directory structure. In addition, a tree object can refer to other tree
+objects, thus creating a directory hierarchy. 
+
+Finally, a "commit" object ties such directory hierarchies together into
+a DAG of revisions - each "commit" is associated with exactly one tree
+(the directory hierarchy at the time of the commit). In addition, a
+"commit" refers to one or more "parent" commit objects that describe the
+history of how we arrived at that directory hierarchy.
+
+As a special case, a commit object with no parents is called the "root"
+object, and is the point of an initial project commit.  Each project
+must have at least one root, and while you can tie several different
+root objects together into one project by creating a commit object which
+has two or more separate roots as its ultimate parents, that's probably
+just going to confuse people.  So aim for the notion of "one root object
+per project", even if git itself does not enforce that. 
+
+Regardless of object type, all objects are share the following
+characteristics: they are all in deflated with zlib, and have a header
+that not only specifies their tag, but also size information about the
+data in the object.  It's worth noting that the SHA1 hash that is used
+to name the object is always the hash of this _compressed_ object, not
+the original data.
+
+As a result, the general consistency of an object can always be tested
 independently of the contents or the type of the object: all objects can
 be validated by verifying that (a) their hashes match the content of the
 file and (b) the object successfully inflates to a stream of bytes that
 forms a sequence of <ascii tag without space> + <space> + <ascii decimal
 size> + <byte\0> + <binary object data>. 
 
-BLOB: A "blob" object is nothing but a binary blob of data, and doesn't
-refer to anything else.  There is no signature or any other verification
-of the data, so while the object is consistent (it _is_ indexed by its
-sha1 hash, so the data itself is certainly correct), it has absolutely
-no other attributes.  No name associations, no permissions.  It is
-purely a blob of data (ie normally "file contents"). 
-
-TREE: The next hierarchical object type is the "tree" object.  A tree
-object is a list of permission/name/blob data, sorted by name.  In other
-words the tree object is uniquely determined by the set contents, and so
-two separate but identical trees will always share the exact same
-object. 
-
-Again, a "tree" object is just a pure data abstraction: it has no
-history, no signatures, no verification of validity, except that the
-contents are again protected by the hash itself.  So you can trust the
-contents of a tree, the same way you can trust the contents of a blob,
-but you don't know where those contents _came_ from. 
-
-Side note on trees: since a "tree" object is a sorted list of
-"filename+content", you can create a diff between two trees without
-actually having to unpack two trees.  Just ignore all common parts, and
-your diff will look right.  In other words, you can effectively (and
-efficiently) tell the difference between any two random trees by O(n)
-where "n" is the size of the difference, rather than the size of the
-tree. 
-
-Side note 2 on trees: since the name of a "blob" depends entirely and
-exclusively on its contents (ie there are no names or permissions
-involved), you can see trivial renames or permission changes by noticing
-that the blob stayed the same.  However, renames with data changes need
-a smarter "diff" implementation. 
+The structured objects can further have their structure and connectivity
+to other objects verified. This is generally done with the "fsck-cache"
+program, which generates a full dependency graph of all objects, and
+verifies their internal consistency (in addition to just verifying their
+superficial consistency through the hash).
+
+The object types in some more detail:
+
+  BLOB: A "blob" object is nothing but a binary blob of data, and
+	doesn't refer to anything else.  There is no signature or any
+	other verification of the data, so while the object is
+	consistent (it _is_ indexed by its sha1 hash, so the data itself
+	is certainly correct), it has absolutely no other attributes. 
+	No name associations, no permissions.  It is purely a blob of
+	data (ie normally "file contents"). 
+
+	In particular, since the blob is entirely defined by its data,
+	if two files in a directory tree (or in multiple different
+	versions of the repository) have the same contents, they will
+	share the same blob object. The object is toally independent
+	of it's location in the directory tree, and renaming a file does
+	not change the object that file is associated with in any way.
+
+  TREE: The next hierarchical object type is the "tree" object.  A tree
+	object is a list of mode/name/blob data, sorted by name. 
+	Alternatively, the mode data may specify a directory mode, in
+	which case instead of naming a blob, that name is associated
+	with another TREE object. 
+
+	Like the "blob" object, a tree object is uniquely determined by
+	the set contents, and so two separate but identical trees will
+	always share the exact same object. This is true at all levels,
+	ie it's true for a "leaf" tree (which does not refer to any
+	other trees, only blobs) as well as for a whole subdirectory.
+
+	For that reason a "tree" object is just a pure data abstraction:
+	it has no history, no signatures, no verification of validity,
+	except that since the contents are again protected by the hash
+	itself, we can trust that the tree is immutable and its contents
+	never change. 
+
+	So you can trust the contents of a tree to be valid, the same
+	way you can trust the contents of a blob, but you don't know
+	where those contents _came_ from.
+
+	Side note on trees: since a "tree" object is a sorted list of
+	"filename+content", you can create a diff between two trees
+	without actually having to unpack two trees.  Just ignore all
+	common parts, and your diff will look right.  In other words,
+	you can effectively (and efficiently) tell the difference
+	between any two random trees by O(n) where "n" is the size of
+	the difference, rather than the size of the tree. 
+
+	Side note 2 on trees: since the name of a "blob" depends
+	entirely and exclusively on its contents (ie there are no names
+	or permissions involved), you can see trivial renames or
+	permission changes by noticing that the blob stayed the same. 
+	However, renames with data changes need a smarter "diff" implementation. 
 
 CHANGESET: The "changeset" object is an object that introduces the
-notion of history into the picture.  In contrast to the other objects,
-it doesn't just describe the physical state of a tree, it describes how
-we got there, and why. 
-
-A "changeset" is defined by the tree-object that it results in, the
-parent changesets (zero, one or more) that led up to that point, and a
-comment on what happened. Again, a changeset is not trusted per se:
-the contents are well-defined and "safe" due to the cryptographically
-strong signatures at all levels, but there is no reason to believe that
-the tree is "good" or that the merge information makes sense. The
-parents do not have to actually have any relationship with the result,
-for example.
-
-Note on changesets: unlike real SCM's, changesets do not contain rename
-information or file mode chane information.  All of that is implicit in
-the trees involved (the result tree, and the result trees of the
-parents), and describing that makes no sense in this idiotic file
-manager.
+	notion of history into the picture.  In contrast to the other
+	objects, it doesn't just describe the physical state of a tree,
+	it describes how we got there, and why. 
+
+	A "changeset" is defined by the tree-object that it results in,
+	the parent changesets (zero, one or more) that led up to that
+	point, and a comment on what happened.  Again, a changeset is
+	not trusted per se: the contents are well-defined and "safe" due
+	to the cryptographically strong signatures at all levels, but
+	there is no reason to believe that the tree is "good" or that
+	the merge information makes sense.  The parents do not have to
+	actually have any relationship with the result, for example. 
+
+	Note on changesets: unlike real SCM's, changesets do not contain
+	rename information or file mode chane information.  All of that
+	is implicit in the trees involved (the result tree, and the
+	result trees of the parents), and describing that makes no sense
+	in this idiotic file manager. 
 
 TRUST: The notion of "trust" is really outside the scope of "git", but
-it's worth noting a few things. First off, since everything is hashed
-with SHA1, you _can_ trust that an object is intact and has not been
-messed with by external sources. So the name of an object uniquely
-identifies a known state - just not a state that you may want to trust.
-
-Furthermore, since the SHA1 signature of a changeset refers to the
-SHA1 signatures of the tree it is associated with and the signatures
-of the parent, a single named changeset specifies uniquely a whole
-set of history, with full contents. You can't later fake any step of
-the way once you have the name of a changeset.
-
-So to introduce some real trust in the system, the only thing you need
-to do is to digitally sign just _one_ special note, which includes the
-name of a top-level changeset.  Your digital signature shows others that
-you trust that changeset, and the immutability of the history of
-changesets tells others that they can trust the whole history.
-
-In other words, you can easily validate a whole archive by just sending
-out a single email that tells the people the name (SHA1 hash) of the top
-changeset, and digitally sign that email using something like GPG/PGP.
-
-In particular, you can also have a separate archive of "trust points" or
-tags, which document your (and other peoples) trust.  You may, of
-course, archive these "certificates of trust" using "git" itself, but
-it's not something "git" does for you. 
-
-Another way of saying the same thing: "git" itself only handles content
+	it's worth noting a few things.  First off, since everything is
+	hashed with SHA1, you _can_ trust that an object is intact and
+	has not been messed with by external sources.  So the name of an
+	object uniquely identifies a known state - just not a state that
+	you may want to trust. 
+
+	Furthermore, since the SHA1 signature of a changeset refers to
+	the SHA1 signatures of the tree it is associated with and the
+	signatures of the parent, a single named changeset specifies
+	uniquely a whole set of history, with full contents.  You can't
+	later fake any step of the way once you have the name of a
+	changeset. 
+
+	So to introduce some real trust in the system, the only thing
+	you need to do is to digitally sign just _one_ special note,
+	which includes the name of a top-level changeset.  Your digital
+	signature shows others that you trust that changeset, and the
+	immutability of the history of changesets tells others that they
+	can trust the whole history. 
+
+	In other words, you can easily validate a whole archive by just
+	sending out a single email that tells the people the name (SHA1
+	hash) of the top changeset, and digitally sign that email using
+	something like GPG/PGP. 
+
+	In particular, you can also have a separate archive of "trust
+	points" or tags, which document your (and other peoples) trust. 
+	You may, of course, archive these "certificates of trust" using
+	"git" itself, but it's not something "git" does for you. 
+
+Another way of saying the last point: "git" itself only handles content
 integrity, the trust has to come from outside. 
 
-	Current Directory Cache (".git/index")
 
-The "current directory cache" is a simple binary file, which contains an
-efficient representation of a virtual directory content at some random
-time.  It does so by a simple array that associates a set of names,
-dates, permissions and content (aka "blob") objects together.  The cache
-is always kept ordered by name, and names are unique at any point in
-time, but the cache has no long-term meaning, and can be partially
-updated at any time. 
 
-In particular, the "current directory cache" certainly does not need to
-be consistent with the current directory contents, but it has two very
-important attributes:
+	The "index" aka "Current Directory Cache" (".git/index")
+
+
+The index is a simple binary file, which contains an efficient
+representation of a virtual directory content at some random time.  It
+does so by a simple array that associates a set of names, dates,
+permissions and content (aka "blob") objects together.  The cache is
+always kept ordered by name, and names are unique (with a few very
+specific rules) at any point in time, but the cache has no long-term
+meaning, and can be partially updated at any time. 
+
+In particular, the index certainly does not need to be consistent with
+the current directory contents (in fact, most operations will depend on
+different ways to make the index _not_ be consistent with the directory
+hierarchy), but it has three very important attributes:
 
  (a) it can re-generate the full state it caches (not just the directory
-     structure: through the "blob" object it can regenerate the data too)
+     structure: it contains pointers to the "blob" objects so that it
+     can regenerate the data too)
 
      As a special case, there is a clear and unambiguous one-way mapping
      from a current directory cache to a "tree object", which can be
@@ -146,23 +218,243 @@ important attributes:
      one time uniquely specifies one and only one "tree" object (but
      has additional data to make it easy to match up that tree object
      with what has happened in the directory)
-    
-
-and
 
  (b) it has efficient methods for finding inconsistencies between that
      cached state ("tree object waiting to be instantiated") and the
      current state. 
 
-Those are the two ONLY things that the directory cache does.  It's a
+ (c) it can additionally efficiently represent information about merge
+     conflicts between different tree objects, allowing each pathname to
+     be associated with sufficient information about the trees involved
+     that you can create a three-way merge between them.
+
+Those are the three ONLY things that the directory cache does.  It's a
 cache, and the normal operation is to re-generate it completely from a
 known tree object, or update/compare it with a live tree that is being
-developed.  If you blow the directory cache away entirely, you haven't
-lost any information as long as you have the name of the tree that it
-described. 
-
-(But directory caches can also have real information in them: in
-particular, they can have the representation of an intermediate tree
-that has not yet been instantiated.  So they do have meaning and usage
-outside of caching - in one sense you can think of the current directory
-cache as being the "work in progress" towards a tree commit).
+developed.  If you blow the directory cache away entirely, you generally
+haven't lost any information as long as you have the name of the tree
+that it described. 
+
+At the same time, the directory index is at the same time also the
+staging area for creating new trees, and creating a new tree always
+involves a controlled modification of the index file.  In particular,
+the index file can have the representation of an intermediate tree that
+has not yet been instantiated.  So the index can be thought of as a
+write-back cache, which can contain dirty information that has not yet
+been written back to the backing store. 
+
+
+
+	The Workflow
+
+
+Generally, all "git" operations work on the index file. Some operations
+work _purely_ on the index file (showing the current state of the
+index), but most operations move data to and from the index file. Either
+from the database or from the working directory. Thus there are four
+main combinations: 
+
+ 1) working directory -> index
+
+	You update the index with information from the working directory
+	with the "update-cache" command.  You generally update the index
+	information by just specifying the filename you want to update,
+	like so:
+
+		update-cache filename
+
+	but to avoid common mistakes with filename globbing etc, the
+	command will not normally add totally new entries or remove old
+	entries, ie it will normally just update existing cache entryes.
+
+	To tell git that yes, you really do realize that certain files
+	no longer exist in the archive, or that new files should be
+	added, you should use the "--remove" and "--add" flags
+	respectively.
+
+	NOTE! A "--remove" flag does _not_ mean that subsequent
+	filenames will necessarily be removed: if the files still exist
+	in your directory structure, the index will be updated with
+	their new status, not removed. The only thing "--remove" means
+	is that update-cache will be considering a removed file to be a
+	valid thing, and if the file really does not exist any more, it
+	will update the index accordingly. 
+
+	As a special case, you can also do "update-cache --refresh",
+	which will refresh the "stat" information of each index to match
+	the current stat information. It will _not_ update the object
+	status itself, and it wil only update the fields that are used
+	to quickly test whether an object still matches its old backing
+	store object.
+
+ 2) index -> object database
+
+	You write your current index file to a "tree" object with the
+	program
+
+		write-tree
+
+	that doesn't come with any options - it will just write out the
+	current index into the set of tree objects that describe that
+	state, and it will return the name of the resulting top-level
+	tree. You can use that tree to re-generate the index at any time
+	by going in the other direction:
+
+ 3) object database -> index
+
+	You read a "tree" file from the object database, and use that to
+	populate (and overwrite - don't do this if your index contains
+	any unsaved state that you might want to restore later!) your
+	current index.  Normal operation is just
+
+		read-tree <sha1 of tree>
+
+	and your index file will now be equivalent to the tree that you
+	saved earlier. However, that is only your _index_ file: your
+	working directory contents have not been modified.
+
+ 4) index -> working directory
+
+	You update your working directory from the index by "checking
+	out" files. This is not a very common operation, since normally
+	you'd just keep your files updated, and rather than write to
+	your working directory, you'd tell the index files about the
+	changes in your working directory (ie "update-cache").
+
+	However, if you decide to jump to a new version, or check out
+	somebody elses version, or just restore a previous tree, you'd
+	populate your index file with read-tree, and then you need to
+	check out the result with
+
+		checkout-cache filename
+
+	or, if you want to check out all of the index, use "-a".
+
+	NOTE! checkout-cache normally refuses to overwrite old files, so
+	if you have an old version of the tree already checked out, you
+	will need to use the "-f" flag (_before_ the "-a" flag or the
+	filename) to _force_ the checkout.
+
+
+Finally, there are a few odds and ends which are not purely moving from
+one representation to the other:
+
+ 5) Tying it all together
+
+	To commit a tree you have instantiated with "write-tree", you'd
+	create a "commit" object that refers to that tree and the
+	history behind it - most notably the "parent" commits that
+	preceded it in history. 
+
+	Normally a "commit" has one parent: the previous state of the
+	tree before a certain change was made. However, sometimes it can
+	have two or more parent commits, in which case we call it a
+	"merge", due to the fact that such a commit brings together
+	("merges") two or more previous states represented by other
+	commits. 
+
+	In other words, while a "tree" represents a particular directory
+	state of a working directory, a "commit" represents that state
+	in "time", and explains how we got there. 
+
+	You create a commit object by giving it the tree that describes
+	the state at the time of the commit, and a list of parents:
+
+		commit-tree <tree> -p <parent> [-p <parent2> ..]
+
+	and then giving the reason for the commit on stdin (either
+	through redirection from a pipe or file, or by just typing it at
+	the tty). 
+
+	commit-tree will return the name of the object that represents
+	that commit, and you should save it away for later use.
+	Normally, you'd commit a new "HEAD" state, and while git doesn't
+	care where you save the note about that state, in practice we
+	tend to just write the result to the file ".git/HEAD", so that
+	we can always see what the last committed state was.
+
+ 6) Examining the data
+
+	You can examine the data represented in the object database and
+	the index with various helper tools. For every object, you can
+	use "cat-file" to examine details about the object:
+
+		cat-file -t <objectname>
+
+	shows the type of the object, and once you have the type (which
+	is usually implicit in where you find the object), you can use
+
+		cat-file blob|tree|commit <objectname>
+
+	to show its contents. NOTE! Trees have binary content, and as a
+	result there is a special helper for showing that content,
+	called "ls-tree", which turns the binary content into a more
+	easily readable form.
+
+	It's especially instructive to look at "commit" objects, since
+	those tend to be small and fairly self-explanatory. In
+	particular, if you follow the convention of having the top
+	commit name in ".git/HEAD", you can do
+
+		cat-file commit $(cat .git/HEAD)
+
+	to see what the top commit was.
+
+ 7) Merging multiple trees
+
+	Git helps you do a three-way merge, which you can expand to
+	n-way by repeating the merge procedure arbitrary times until you
+	finally "commit" the state.  The normal situation is that you'd
+	only do one three-way merge (two parents), and commit it, but if
+	you like to, you can do multiple parents in one go.
+
+	To do a three-way merge, you need the two sets of "commit"
+	objects that you want to merge, use those to find the closest
+	common parent (a third "commit" object), and then use those
+	commit objects to find the state of the directory ("tree"
+	object) at these points. 
+
+	To get the "base" for the merge, you first look up the common
+	parent of two commits with
+
+		merge-base <commit1> <commit2>
+
+	which will return you the commit they are both based on.  You
+	should now look up the "tree" objects of those commits, which
+	you can easily do with (for example)
+
+		cat-file commit <commitname> | head -1
+
+	since the tree object information is always the first line in a
+	commit object. 
+
+	Once you know the three trees you are going to merge (the one
+	"original" tree, aka the common case, and the two "result" trees,
+	aka the branches you want to merge), you do a "merge" read into
+	the index. This will throw away your old index contents, so you
+	should make sure that you've committed those - in fact you would
+	normally always do a merge against your last commit (which
+	should thus match what you have in your current index anyway).
+	To do the merge, do
+
+		read-tree -m <origtree> <target1tree> <target2tree>
+
+	which will do all trivial merge operations for you directly in
+	the index file, and you can just write the result out with
+	"write-tree". 
+
+	NOTE! Because the merge is done in the index file, and not in
+	your working directory, your working directory will no longer
+	match your index. You can use "checkout-cache -f -a" to make the
+	effect of the merge be seen in your working directory.
+
+	NOTE2! Sadly, many merges aren't trivial. If there are files
+	that have been added.moved or removed, or if both branches have
+	modified the same file, you will be left with an index tree that
+	contains "merge entries" in it. Such an index tree can _NOT_ be
+	written out to a tree object, and you will have to resolve any
+	such merge clashes using other tools before you can write out
+	the result.
+
+	[ fixme: talk about resolving merges here ]
+