+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 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 gitlink:git-update-index[1] command. You
+generally update the index information by just specifying the filename
+you want to update, like so:
+
+ git-update-index filename
+
+but to avoid common mistakes with filename globbing etc, the command
+will not normally add totally new entries or remove old entries,
+i.e. it will normally just update existing cache entries.
+
+To tell git that yes, you really do realize that certain files no
+longer exist, 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 `git-update-index --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 will 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
+
+ git-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
+
+ git-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 (i.e. `git-update-index`).
+
+However, if you decide to jump to a new version, or check out somebody
+else's 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
+
+ git-checkout-index filename
+
+or, if you want to check out all of the index, use `-a`.
+
+NOTE! git-checkout-index 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 "git-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:
+
+ git-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).
+
+git-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 pointed at by `.git/HEAD`, so that we can always see
+what the last committed state was.
+
+Here is an ASCII art by Jon Loeliger that illustrates how
+various pieces fit together.
+
+------------
+
+ commit-tree
+ commit obj
+ +----+
+ | |
+ | |
+ V V
+ +-----------+
+ | Object DB |
+ | Backing |
+ | Store |
+ +-----------+
+ ^
+ write-tree | |
+ tree obj | |
+ | | read-tree
+ | | tree obj
+ V
+ +-----------+
+ | Index |
+ | "cache" |
+ +-----------+
+ update-index ^
+ blob obj | |
+ | |
+ checkout-index -u | | checkout-index
+ stat | | blob obj
+ V
+ +-----------+
+ | Working |
+ | Directory |
+ +-----------+
+
+------------
+
+
+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
+gitlink:git-cat-file[1] to examine details about the
+object:
+
+ git-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
+
+ git-cat-file blob|tree|commit|tag <objectname>
+
+to show its contents. NOTE! Trees have binary content, and as a result
+there is a special helper for showing that content, called
+`git-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
+
+ git-cat-file commit 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
+
+ git-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)
+
+ git-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 complain if it has to 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
+
+ git-read-tree -m -u <origtree> <yourtree> <targettree>
+
+which will do all trivial merge operations for you directly in the
+index file, and you can just write the result out with
+`git-write-tree`.
+
+Historical note. We did not have `-u` facility when this
+section was first written, so we used to warn that
+the merge is done in the index file, not in your
+working tree, and your working tree will not match your
+index after this step.
+This is no longer true. The above command, thanks to `-u`
+option, updates your working tree with the merge results for
+paths that have been trivially merged.
+
+
+8) Merging multiple trees, continued
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+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.
+
+You can examine such index state with `git-ls-files --unmerged`
+command. An example:
+
+------------------------------------------------
+$ git-read-tree -m $orig HEAD $target
+$ git-ls-files --unmerged
+100644 263414f423d0e4d70dae8fe53fa34614ff3e2860 1 hello.c
+100644 06fa6a24256dc7e560efa5687fa84b51f0263c3a 2 hello.c
+100644 cc44c73eb783565da5831b4d820c962954019b69 3 hello.c
+------------------------------------------------
+
+Each line of the `git-ls-files --unmerged` output begins with
+the blob mode bits, blob SHA1, 'stage number', and the
+filename. The 'stage number' is git's way to say which tree it
+came from: stage 1 corresponds to `$orig` tree, stage 2 `HEAD`
+tree, and stage3 `$target` tree.
+
+Earlier we said that trivial merges are done inside
+`git-read-tree -m`. For example, if the file did not change
+from `$orig` to `HEAD` nor `$target`, or if the file changed
+from `$orig` to `HEAD` and `$orig` to `$target` the same way,
+obviously the final outcome is what is in `HEAD`. What the
+above example shows is that file `hello.c` was changed from
+`$orig` to `HEAD` and `$orig` to `$target` in a different way.
+You could resolve this by running your favorite 3-way merge
+program, e.g. `diff3` or `merge`, on the blob objects from
+these three stages yourself, like this:
+
+------------------------------------------------
+$ git-cat-file blob 263414f... >hello.c~1
+$ git-cat-file blob 06fa6a2... >hello.c~2
+$ git-cat-file blob cc44c73... >hello.c~3
+$ merge hello.c~2 hello.c~1 hello.c~3
+------------------------------------------------
+
+This would leave the merge result in `hello.c~2` file, along
+with conflict markers if there are conflicts. After verifying
+the merge result makes sense, you can tell git what the final
+merge result for this file is by:
+
+ mv -f hello.c~2 hello.c
+ git-update-index hello.c
+
+When a path is in unmerged state, running `git-update-index` for
+that path tells git to mark the path resolved.
+
+The above is the description of a git merge at the lowest level,
+to help you understand what conceptually happens under the hood.
+In practice, nobody, not even git itself, uses three `git-cat-file`
+for this. There is `git-merge-index` program that extracts the
+stages to temporary files and calls a "merge" script on it:
+
+ git-merge-index git-merge-one-file hello.c
+
+and that is what higher level `git resolve` is implemented with.