Parseopt wraps arguments in a pair of angular brackets by default,
signifying that the user needs to replace it with a value of the
documented type. Remove the pairs from the option definitions to
duplication and confusion.
Signed-off-by: Rene Scharfe <l.s.r@web.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Don't translate the argument specification for --chmod; "+x" and "-x"
are the literal strings that the commands accept.
Separate alternatives using a pipe character instead of a slash, for
consistency.
Use the flag PARSE_OPT_LITERAL_ARGHELP to prevent parseopt from adding a
pair of angular brackets around the argument help string, as that would
wrongly indicate that users need to replace the literal strings with
some kind of value.
Signed-off-by: Rene Scharfe <l.s.r@web.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
The option help text for the force-with-lease option to "git push"
reads like this:
$ git push -h 2>&1 | grep -e force-with-lease
--force-with-lease[=<refname>:<expect>]
which comes from having N_("refname>:<expect") as the argument help
text in the source code, with an aparent lack of "<" and ">" at both
ends.
It turns out that parse-options machinery takes the whole string and
encloses it inside a pair of "<>", to make it easier for majority
cases that uses a single token placeholder.
The help string was written in a funnily unbalanced way knowing that
the end result would balance out, by somebody who forgot the
presence of PARSE_OPT_LITERAL_ARGHELP, which is the escape hatch
mechanism designed to help such a case. We just should use the
official escape hatch instead.
Because ":<expect>" part can be omitted to ask Git to guess, it may
be more correct to spell it as "<refname>[:<expect>]", but that is
not the focus of this topic.
Signed-off-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Helped-by: René Scharfe <l.s.r@web.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
The recursive merge strategy did not properly ensure there was no
change between HEAD and the index before performing its operation,
which has been corrected.
* en/dirty-merge-fixes:
merge: fix misleading pre-merge check documentation
merge-recursive: enforce rule that index matches head before merging
t6044: add more testcases with staged changes before a merge is invoked
merge-recursive: fix assumption that head tree being merged is HEAD
merge-recursive: make sure when we say we abort that we actually abort
t6044: add a testcase for index matching head, when head doesn't match HEAD
t6044: verify that merges expected to abort actually abort
index_has_changes(): avoid assuming operating on the_index
read-cache.c: move index_has_changes() from merge.c
"git rebase --rebase-merges" mode now handles octopus merges as
well.
* js/rebase-merge-octopus:
rebase --rebase-merges: adjust man page for octopus support
rebase --rebase-merges: add support for octopus merges
merge: allow reading the merge commit message from a file
"git gc --auto" opens file descriptors for the packfiles before
spawning "git repack/prune", which would upset Windows that does
not want a process to work on a file that is open by another
process. The issue has been worked around.
* kg/gc-auto-windows-workaround:
gc --auto: release pack files before auto packing
For a large tree, the index needs to hold many cache entries
allocated on heap. These cache entries are now allocated out of a
dedicated memory pool to amortize malloc(3) overhead.
* jm/cache-entry-from-mem-pool:
block alloc: add validations around cache_entry lifecyle
block alloc: allocate cache entries from mem_pool
mem-pool: fill out functionality
mem-pool: add life cycle management functions
mem-pool: only search head block for available space
block alloc: add lifecycle APIs for cache_entry structs
read-cache: teach make_cache_entry to take object_id
read-cache: teach refresh_cache_entry to take istate
"git fetch" learned a new option "--negotiation-tip" to limit the
set of commits it tells the other end as "have", to reduce wasted
bandwidth and cycles, which would be helpful when the receiving
repository has a lot of refs that have little to do with the
history at the remote it is fetching from.
* jt/fetch-nego-tip:
fetch-pack: support negotiation tip whitelist
Parsing of -L[<N>][,[<M>]] parameters "git blame" and "git log"
take has been tweaked.
* is/parsing-line-range:
log: prevent error if line range ends past end of file
blame: prevent error if range ends past end of file
"git checkout" and "git worktree add" learned to honor
checkout.defaultRemote when auto-vivifying a local branch out of a
remote tracking branch in a repository with multiple remotes that
have tracking branches that share the same names.
* ab/checkout-default-remote:
checkout & worktree: introduce checkout.defaultRemote
checkout: add advice for ambiguous "checkout <branch>"
builtin/checkout.c: use "ret" variable for return
checkout: pass the "num_matches" up to callers
checkout.c: change "unique" member to "num_matches"
checkout.c: introduce an *_INIT macro
checkout.h: wrap the arguments to unique_tracking_name()
checkout tests: index should be clean after dwim checkout
"git fsck" learns to make sure the optional commit-graph file is in
a sane state.
* ds/commit-graph-fsck: (23 commits)
coccinelle: update commit.cocci
commit-graph: update design document
gc: automatically write commit-graph files
commit-graph: add '--reachable' option
commit-graph: use string-list API for input
fsck: verify commit-graph
commit-graph: verify contents match checksum
commit-graph: test for corrupted octopus edge
commit-graph: verify commit date
commit-graph: verify generation number
commit-graph: verify parent list
commit-graph: verify root tree OIDs
commit-graph: verify objects exist
commit-graph: verify corrupt OID fanout and lookup
commit-graph: verify required chunks are present
commit-graph: verify catches corrupt signature
commit-graph: add 'verify' subcommand
commit-graph: load a root tree from specific graph
commit: force commit to parse from object database
commit-graph: parse commit from chosen graph
...
Conversion from uchar[40] to struct object_id continues.
* bc/object-id:
pretty: switch hard-coded constants to the_hash_algo
sha1-file: convert constants to uses of the_hash_algo
log-tree: switch GIT_SHA1_HEXSZ to the_hash_algo->hexsz
diff: switch GIT_SHA1_HEXSZ to use the_hash_algo
builtin/merge-recursive: make hash independent
builtin/merge: switch to use the_hash_algo
builtin/fmt-merge-msg: make hash independent
builtin/update-index: simplify parsing of cacheinfo
builtin/update-index: convert to using the_hash_algo
refs/files-backend: use the_hash_algo for writing refs
sha1-name: use the_hash_algo when parsing object names
strbuf: allocate space with GIT_MAX_HEXSZ
commit: express tree entry constants in terms of the_hash_algo
hex: switch to using the_hash_algo
tree-walk: replace hard-coded constants with the_hash_algo
cache: update object ID functions for the_hash_algo
When a user fetches:
- at least one up-to-date ref and at least one non-up-to-date ref,
- using HTTP with protocol v0 (or something else that uses the fetch
command of a remote helper)
some refs might not be updated after the fetch.
This bug was introduced in commit 989b8c4452 ("fetch-pack: put shallow
info in output parameter", 2018-06-28) which allowed transports to
report the refs that they have fetched in a new out-parameter
"fetched_refs". If they do so, transport_fetch_refs() makes this
information available to its caller.
Users of "fetched_refs" rely on the following 3 properties:
(1) it is the complete list of refs that was passed to
transport_fetch_refs(),
(2) it has shallow information (REF_STATUS_REJECT_SHALLOW set if
relevant), and
(3) it has updated OIDs if ref-in-want was used (introduced after
989b8c4452).
In an effort to satisfy (1), whenever transport_fetch_refs()
filters the refs sent to the transport, it re-adds the filtered refs to
whatever the transport supplies before returning it to the user.
However, the implementation in 989b8c4452 unconditionally re-adds the
filtered refs without checking if the transport refrained from reporting
anything in "fetched_refs" (which it is allowed to do), resulting in an
incomplete list, no longer satisfying (1).
An earlier effort to resolve this [1] solved the issue by readding the
filtered refs only if the transport did not refrain from reporting in
"fetched_refs", but after further discussion, it seems that the better
solution is to revert the API change that introduced "fetched_refs".
This API change was first suggested as part of a ref-in-want
implementation that allowed for ref patterns and, thus, there could be
drastic differences between the input refs and the refs actually fetched
[2]; we eventually decided to only allow exact ref names, but this API
change remained even though its necessity was decreased.
Therefore, revert this API change by reverting commit 989b8c4452, and
make receive_wanted_refs() update the OIDs in the sought array (like how
update_shallow() updates shallow information in the sought array)
instead. A test is also included to show that the user-visible bug
discussed at the beginning of this commit message no longer exists.
[1] https://public-inbox.org/git/20180801171806.GA122458@google.com/
[2] https://public-inbox.org/git/86a128c5fb710a41791e7183207c4d64889f9307.1485381677.git.jonathantanmy@google.com/
Signed-off-by: Jonathan Tan <jonathantanmy@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Switch to the _DUP variant of string_list for remote_branches to allow
string_list_clear() to release the allocated memory at the end, and
actually call that function. Free the util pointer as well; it is
allocated in read_remote_branches().
NB: This string_list is empty until read_remote_branches() is called
via for_each_ref(), so there is no need to clean it up when returning
before that point.
Signed-off-by: Rene Scharfe <l.s.r@web.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
These extra comments should be make it easier to understand how to use
locks in pack-objects delta search code. For reference, see
8ecce684a3 (basic threaded delta search - 2007-09-06)
384b32c09b (pack-objects: fix threaded load balancing - 2007-12-08)
50f22ada52 (threaded pack-objects: Use condition... - 2007-12-16)
Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Code clean-up.
* hs/push-cert-check-cleanup:
gpg-interface: make parse_gpg_output static and remove from interface header
builtin/receive-pack: use check_signature from gpg-interface
Partial clone support of "git clone" has been updated to correctly
validate the objects it receives from the other side. The server
side has been corrected to send objects that are directly
requested, even if they may match the filtering criteria (e.g. when
doing a "lazy blob" partial clone).
* jt/partial-clone-fsck-connectivity:
clone: check connectivity even if clone is partial
upload-pack: send refs' objects despite "filter"
"git fetch" failed to correctly validate the set of objects it
received when making a shallow history deeper, which has been
corrected.
* jt/connectivity-check-after-unshallow:
fetch-pack: write shallow, then check connectivity
fetch-pack: implement ref-in-want
fetch-pack: put shallow info in output parameter
fetch: refactor to make function args narrower
fetch: refactor fetch_refs into two functions
fetch: refactor the population of peer ref OIDs
upload-pack: test negotiation with changing repository
upload-pack: implement ref-in-want
test-pkt-line: add unpack-sideband subcommand
When we initially added the strbuf_readlink() function in
b11b7e13f4 (Add generic 'strbuf_readlink()' helper function,
2008-12-17), the point was that we generally have a _guess_
as to the correct size based on the stat information, but we
can't necessarily trust it.
Over the years, a few callers have grown up that simply pass
in 0, even though they have the stat information. Let's have
them pass in their hint for consistency (and in theory
efficiency, since it may avoid an extra resize/syscall loop,
but neither location is probably performance critical).
Note that st.st_size is actually an off_t, so in theory we
need xsize_t() here. But none of the other callsites use it,
and since this is just a hint, it doesn't matter either way
(if we wrap we'll simply start with a too-small hint and
then eventually complain when we cannot allocate the
memory).
Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
When performing tag following, in addition to using the server's
"include-tag" capability to send tag objects (and emulating it if the
server does not support that capability), "git fetch" relies upon the
presence of refs/tags/* entries in the initial ref advertisement to
locally create refs pointing to the aforementioned tag objects. When
using protocol v2, refs/tags/* entries in the initial ref advertisement
may be suppressed by a ref-prefix argument, leading to the tag object
being downloaded, but the ref not being created.
Commit dcc73cf7ff ("fetch: generate ref-prefixes when using a configured
refspec", 2018-05-18) ensured that "refs/tags/" is always sent as a ref
prefix when "git fetch" is invoked with no refspecs, but not when "git
fetch" is invoked with refspecs. Extend that functionality to make it
work in both situations.
This also necessitates a change another test which tested ref
advertisement filtering using tag refs - since tag refs are sent by
default now, the test has been switched to using branch refs instead.
Signed-off-by: Jonathan Tan <jonathantanmy@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
When submitting a revised version of a patch or series, it can be
helpful (to reviewers) to include a summary of changes since the
previous attempt in the form of an interdiff, typically in the cover
letter. However, it is occasionally useful, despite making for a noisy
read, to insert an interdiff into the commentary section of the lone
patch of a 1-patch series.
Therefore, extend "git format-patch --interdiff=<prev>" to insert an
interdiff into the commentary section of a lone patch rather than
requiring a cover letter. The interdiff is indented to avoid confusing
git-am and human readers into considering it part of the patch proper.
Implementation note: Generating an interdiff for insertion into the
commentary section of a patch which itself is currently being generated
requires invoking the diffing machinery recursively. However, the
machinery does not (presently) support this since it uses global state.
Consequently, we need to take care to stash away the state of the
in-progress operation while generating the interdiff, and restore it
after.
Signed-off-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
A future change will allow "git format-patch --interdiff=<prev> -1" to
insert an interdiff into the commentary section of the lone patch of a
1-patch series. However, to prevent the inserted interdiff from
confusing git-am, as well as human readers, it needs to be indented.
Therefore, teach show_interdiff() how to indent.
Signed-off-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
The --interdiff option introduces the embedded interdiff generically as
"Interdiff:", however, we can do better when --reroll-count is specified
by emitting "Interdiff against v{n}:" instead.
Signed-off-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
When submitting a revised version of a patch series, it can be helpful
(to reviewers) to include a summary of changes since the previous
attempt in the form of an interdiff, however, doing so involves manually
copy/pasting the diff into the cover letter.
Add an --interdiff option to automate this process. The argument to
--interdiff specifies the tip of the previous attempt against which to
generate the interdiff. For example:
git format-patch --cover-letter --interdiff=v1 -3 v2
The previous attempt and the patch series being formatted must share a
common base.
Signed-off-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
make_cover_letter() returns early when it lacks sufficient state to emit
a diffstat, which makes it difficult to extend the function to reliably
emit additional generated content. Work around this shortcoming by
factoring diffstat-printing logic out to its own function and calling it
as needed without otherwise inhibiting normal control flow.
Signed-off-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Most of these are straight forward. GETTEXT_POISON does catch the last
string in cmd_pack_objects(), but since this is --progress output, it's
not supposed to be machine-readable.
Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Many messages will be marked for translation in the following
commits. This commit updates some of them to be more consistent and
reduce diff noise in those commits. Changes are
- keep the first letter of die(), error() and warning() in lowercase
- no full stop in die(), error() or warning() if it's single sentence
messages
- indentation
- some messages are turned to BUG(), or prefixed with "BUG:" and will
not be marked for i18n
- some messages are improved to give more information
- some messages are broken down by sentence to be i18n friendly
(on the same token, combine multiple warning() into one big string)
- the trailing \n is converted to printf_ln if possible, or deleted
if not redundant
- errno_errno() is used instead of explicit strerror()
Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Let's start with some background about oe_delta_size() and
oe_set_delta_size(). If you already know, skip the next paragraph.
These two are added in 0aca34e826 (pack-objects: shrink delta_size
field in struct object_entry - 2018-04-14) to help reduce 'struct
object_entry' size. The delta size field in this struct is reduced to
only contain max 1MB. So if any new delta is produced and larger than
1MB, it's dropped because we can't really save such a large size
anywhere. Fallback is provided in case existing packfiles already have
large deltas, then we can retrieve it from the pack.
While this should help small machines repacking large repos without
large deltas (i.e. less memory pressure), dropping large deltas during
the delta selection process could end up with worse pack files. And if
existing packfiles already have >1MB delta and pack-objects is
instructed to not reuse deltas, all of them will be dropped on the
floor, and the resulting pack would be definitely bigger.
There is also a regression in terms of CPU/IO if we have large on-disk
deltas because fallback code needs to parse the pack every time the
delta size is needed and just access to the mmap'd pack data is enough
for extra page faults when memory is under pressure.
Both of these issues were reported on the mailing list. Here's some
numbers for comparison.
Version Pack (MB) MaxRSS(kB) Time (s)
------- --------- ---------- --------
2.17.0 5498 43513628 2494.85
2.18.0 10531 40449596 4168.94
This patch provides a better fallback that is
- cheaper in terms of cpu and io because we won't have to read
existing pack files as much
- better in terms of pack size because the pack heuristics is back to
2.17.0 time, we do not drop large deltas at all
If we encounter any delta (on-disk or created during try_delta phase)
that is larger than the 1MB limit, we stop using delta_size_ field for
this because it can't contain such size anyway. A new array of delta
size is dynamically allocated and can hold all the deltas that 2.17.0
can. This array only contains delta sizes that delta_size_ can't
contain.
With this, we do not have to drop deltas in try_delta() anymore. Of
course the downside is we use slightly more memory, even compared to
2.17.0. But since this is considered an uncommon case, a bit more
memory consumption should not be a problem.
Delta size limit is also raised from 1MB to 16MB to better cover
common case and avoid that extra memory consumption (99.999% deltas in
this reported repo are under 12MB; Jeff noted binary artifacts topped
out at about 3MB in some other private repos). Other fields are
shuffled around to keep this struct packed tight. We don't use more
memory in common case even with this limit update.
A note about thread synchronization. Since this code can be run in
parallel during delta searching phase, we need a mutex. The realloc
part in packlist_alloc() is not protected because it only happens
during the object counting phase, which is always single-threaded.
Access to e->delta_size_ (and by extension
pack->delta_size[e - pack->objects]) is unprotected as before, the
thread scheduler in pack-objects must make sure "e" is never updated
by two different threads.
The area under the new lock is as small as possible, avoiding locking
at all in common case, since lock contention with high thread count
could be expensive (most blobs are small enough that delta compute
time is short and we end up taking the lock very often). The previous
attempt to always hold a lock in oe_delta_size() and
oe_set_delta_size() increases execution time by 33% when repacking
linux.git with with 40 threads.
Reported-by: Elijah Newren <newren@gmail.com>
Helped-by: Elijah Newren <newren@gmail.com>
Helped-by: Jeff King <peff@peff.net>
Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
There are several commit walks in the codebase. Group them together into
a new commit-reach.c file and corresponding header. After we group these
walks into one place, we can reduce duplicate logic by calling
equivalent methods.
The ref_newer() method is used by 'git push -f' to check if a force-push
is necessary. By making the method public, we make it possible to test
the method directly without setting up an envieronment where a 'git
push' call makes sense.
Signed-off-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
These methods are now declared in commit-reach.h. Remove them from
commit.h and add new include statements in all files that require these
declarations.
Signed-off-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Teach clone to send a list of ref-prefixes, when using protocol v2, to
allow the server to filter out irrelevant references from the
ref-advertisement. This reduces wasted time and bandwidth when cloning
repositories with a larger number of references.
Signed-off-by: Brandon Williams <bmwill@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
If a 'git repack' command replaces existing packfiles, then we must
clear the existing multi-pack-index before moving the packfiles it
references.
Signed-off-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
In anticipation of writing multi-pack-indexes, add a skeleton
'git multi-pack-index write' subcommand and send the options to a
write_midx_file() method. Also create a skeleton test script that
tests the 'write' subcommand.
Signed-off-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
This new 'git multi-pack-index' builtin will be the plumbing access
for writing, reading, and checking multi-pack-index files. The
initial implementation is a no-op.
Signed-off-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
This was added as a NEEDSWORK in c3c36d7de2 (replace-object:
check_replace_refs is safe in multi repo environment, 2018-04-11),
waiting for a calmer period. Since doing so now doesn't conflict
with anything in 'pu', it seems as good a time as any.
Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Tighten the API to make it harder to misuse in-tree .gitmodules
file, even though it shares the same syntax with configuration
files, to read random configuration items from it.
* ao/config-from-gitmodules:
submodule-config: reuse config_from_gitmodules in repo_read_gitmodules
submodule-config: pass repository as argument to config_from_gitmodules
submodule-config: make 'config_from_gitmodules' private
submodule-config: add helper to get 'update-clone' config from .gitmodules
submodule-config: add helper function to get 'fetch' config from .gitmodules
config: move config_from_gitmodules to submodule-config.c
The "-l" option in "git branch -l" is an unfortunate short-hand for
"--create-reflog", but many users, both old and new, somehow expect
it to be something else, perhaps "--list". This step warns when "-l"
is used as a short-hand for "--create-reflog" and warns about the
future repurposing of the it when it is used.
* jk/branch-l-0-deprecation:
branch: deprecate "-l" option
t: switch "branch -l" to "branch --create-reflog"
t3200: unset core.logallrefupdates when testing reflog creation
"git grep" learned the "--column" option that gives not just the
line number but the column number of the hit.
* tb/grep-column:
contrib/git-jump/git-jump: jump to exact location
grep.c: add configuration variables to show matched option
builtin/grep.c: add '--column' option to 'git-grep(1)'
grep.c: display column number of first match
grep.[ch]: extend grep_opt to allow showing matched column
grep.c: expose {,inverted} match column in match_line()
Documentation/config.txt: camel-case lineNumber for consistency
The effort to move globals to per-repository in-core structure
continues.
* jt/remove-pack-bitmap-global:
pack-bitmap: add free function
pack-bitmap: remove bitmap_git global variable
Recently added "--base" option to "git format-patch" command did
not correctly generate prereq patch ids.
* xy/format-patch-prereq-patch-id-fix:
format-patch: clear UNINTERESTING flag before prepare_bases
"git submodule" did not correctly adjust core.worktree setting that
indicates whether/where a submodule repository has its associated
working tree across various state transitions, which has been
corrected.
* sb/submodule-core-worktree:
submodule deinit: unset core.worktree
submodule: ensure core.worktree is set after update
submodule: unset core.worktree if no working tree is present
The conversion to pass "the_repository" and then "a_repository"
throughout the object access API continues.
* sb/object-store-grafts:
commit: allow lookup_commit_graft to handle arbitrary repositories
commit: allow prepare_commit_graft to handle arbitrary repositories
shallow: migrate shallow information into the object parser
path.c: migrate global git_path_* to take a repository argument
cache: convert get_graft_file to handle arbitrary repositories
commit: convert read_graft_file to handle arbitrary repositories
commit: convert register_commit_graft to handle arbitrary repositories
commit: convert commit_graft_pos() to handle arbitrary repositories
shallow: add repository argument to is_repository_shallow
shallow: add repository argument to check_shallow_file_for_update
shallow: add repository argument to register_shallow
shallow: add repository argument to set_alternate_shallow_file
commit: add repository argument to lookup_commit_graft
commit: add repository argument to prepare_commit_graft
commit: add repository argument to read_graft_file
commit: add repository argument to register_commit_graft
commit: add repository argument to commit_graft_pos
object: move grafts to object parser
object-store: move object access functions to object-store.h
