apply: fix an incomplete comment in check_patch()

This check is not only about type-change (for which it would be
sufficient to check only was_deleted()) but is also about a swap
rename.  Otherwise to_be_deleted() check is not justified.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: a bit more comments on PATH_TO_BE_DELETED

The code is littered with to_be_deleted() whose purpose is not so clear.
Describe where it matters.  Also remove an extra space before "#define"
that snuck in by mistake at 7fac0ee (builtin-apply: keep information about
files to be deleted, 2009-04-11).

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: clear_image() clears things a bit more

The clear_image() function did not clear the line table in the image
structure; this does not matter for the current callers, as the function
is only called from the codepaths that deal with binary patches where the
line table is never populated, and the codepaths that do populate the line
table free it themselves.

But it will start to matter when we introduce a codepath to retry a failed
patch, so make sure it clears and frees everything.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: refactor read_file_or_gitlink()

Reading a blob out of the object store does not have to require that the
caller has a cache entry for it.

Create a read_blob_object() helper function that takes the object name and
mode, and use it to reimplement the original function as a thin wrapper to
it.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: factor out checkout_target() helper function

When a patch wants to touch a path, if the path exists in the index
but is missing in the working tree, "git apply --index" checks out
the file to the working tree from the index automatically and then
applies the patch.

Split this logic out to a separate helper function.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: split load_preimage() helper function out

Given a patch for a single path, the function apply_data() reads the
preimage in core, and applies the change represented in the patch.

Separate out the first part that reads the preimage into a separate
helper function load_preimage().

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: refactor "previous patch" logic

The code to grab the result of application of a previous patch in the
input was mixed with error message generation for a case where a later
patch tries to modify contents of a path that has been removed.

The same code is duplicated elsewhere in the code.  Introduce a helper
to clarify what is going on.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: further split load_preimage()

load_preimage() is very specific to grab the current contents for
the path given by patch->old_name.  Split the logic that grabs the
contents for a path out of it into a separate load_patch_target()
function.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: move check_to_create_blob() closer to its sole caller

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: move "already exists" logic to check_to_create()

The check_to_create_blob() function used to check only the case
where we are applying to the working tree.  Rename the function to
check_to_create() and make it also responsible for checking the case
where we apply to the index.  Also make its caller responsible for
issuing an error message.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: accept -3/--3way command line option

Begin teaching the three-way merge fallback logic "git am -3" uses
to the underlying "git apply".  It only implements the command line
parsing part, and does not do anything interesting yet, other than
making sure that "--reject" and "--3way" are not given together, and
making "--3way" imply "--index".

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: fall back on three-way merge

Grab the preimage blob the patch claims to be based on out of the object
store, apply the patch, and then call three-way-merge function.  This step
still does not plug the actual three-way merge logic yet, but we are
getting there.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: plug the three-way merge logic in

When a patch does not apply to what we have, but we know the preimage the
patch was made against, we apply the patch to the preimage to compute what
the patch author wanted the result to look like, and attempt a three-way
merge between the result and our version, using the intended preimage as
the base version.

When we are applying the patch using the index, we would additionally need
to add the object names of these three blobs involved in the merge, which
is not yet done in this step, but we add a field to "struct patch" so that
later write-out step can use it.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: move verify_index_match() higher

We will be adding another caller of this function in a later patch.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: --3way with add/add conflict

When a patch wants to create a path, but we already have it in our
current state, pretend as if the patch and we independently added
the same path and cause add/add conflict, so that the user can
resolve it just like "git merge" in the same situation.

For that purpose, implement load_current() in terms of the
load_patch_target() helper introduced earlier to read the current
contents from the path given by patch->new_name (patch->old_name is
NULL for a creation patch).

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: register conflicted stages to the index

Now we have all the necessary logic to fall back on three-way merge when
the patch does not cleanly apply, insert the conflicted entries to the
index as appropriate.  This obviously triggers only when the "--index"
option is used.

When we fall back to three-way merge and some of the merges fail, just
like the case where the "--reject" option was specified and we had to
write some "*.rej" files out for unapplicable patches, exit the command
with non-zero status without showing the diffstat and summary.  Otherwise
they would make the list of problematic paths scroll off the display.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: allow rerere() to work on --3way results

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply: document --3way option

Signed-off-by: Junio C Hamano <gitster@pobox.com>
apply --3way: tests

Signed-off-by: Junio C Hamano <gitster@pobox.com>
rerere: make rr-cache fanout directory honor umask

This is the last remaining call to mkdir(2) that restricts the permission
bits by passing 0755.  Just use the same mkdir_in_gitdir() used to create
the leaf directories.

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