batch check whether submodule needs pushing into one call
We run a command for each sha1 change in a submodule. This is
unnecessary since we can simply batch all sha1's we want to check into
one command. Lets do it so we can speedup the check when many submodule
changes are in need of checking.
Signed-off-by: Heiko Voigt <hvoigt@hvoigt.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
serialize collection of refs that contain submodule changes
We are iterating over each pushed ref and want to check whether it
contains changes to submodules. Instead of immediately checking each ref
lets first collect them and then do the check for all of them in one
revision walk.
Signed-off-by: Heiko Voigt <hvoigt@hvoigt.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
To check whether a submodule needs to be pushed we need to collect all
changed submodules. Lets collect them first and then execute the
possibly expensive test whether certain revisions are already pushed
only once per submodule.
There is further potential for optimization since we can assemble one
command and only issued that instead of one call for each remote ref in
the submodule.
Signed-off-by: Heiko Voigt <hvoigt@hvoigt.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
It is a common mistake to say "git blame --reverse OLD path",
expecting that the command line is dwimmed as if asking how lines
in path in an old revision OLD have survived up to the current
commit.
* jc/blame-reverse:
blame: dwim "blame --reverse OLD" as "blame --reverse OLD.."
blame: improve diagnosis for "--reverse NEW"
The existing "git fetch --depth=<n>" option was hard to use
correctly when making the history of an existing shallow clone
deeper. A new option, "--deepen=<n>", has been added to make this
easier to use. "git clone" also learned "--shallow-since=<date>"
and "--shallow-exclude=<tag>" options to make it easier to specify
"I am interested only in the recent N months worth of history" and
"Give me only the history since that version".
* nd/shallow-deepen: (27 commits)
fetch, upload-pack: --deepen=N extends shallow boundary by N commits
upload-pack: add get_reachable_list()
upload-pack: split check_unreachable() in two, prep for get_reachable_list()
t5500, t5539: tests for shallow depth excluding a ref
clone: define shallow clone boundary with --shallow-exclude
fetch: define shallow boundary with --shallow-exclude
upload-pack: support define shallow boundary by excluding revisions
refs: add expand_ref()
t5500, t5539: tests for shallow depth since a specific date
clone: define shallow clone boundary based on time with --shallow-since
fetch: define shallow boundary with --shallow-since
upload-pack: add deepen-since to cut shallow repos based on time
shallow.c: implement a generic shallow boundary finder based on rev-list
fetch-pack: use a separate flag for fetch in deepening mode
fetch-pack.c: mark strings for translating
fetch-pack: use a common function for verbose printing
fetch-pack: use skip_prefix() instead of starts_with()
upload-pack: move rev-list code out of check_non_tip()
upload-pack: make check_non_tip() clean things up on error
upload-pack: tighten number parsing at "deepen" lines
...
The command-line completion script (in contrib/) learned to
complete "git cmd ^mas<HT>" to complete the negative end of
reference to "git cmd ^master".
* cp/completion-negative-refs:
completion: support excluding refs
When we started cURL to talk to imap server when a new enough
version of cURL library is available, we forgot to explicitly add
imap(s):// before the destination. To some folks, that didn't work
and the library tried to make HTTP(s) requests instead.
* ak/curl-imap-send-explicit-scheme:
imap-send: Tell cURL to use imap:// or imaps://
"git pack-objects" in a repository with many packfiles used to
spend a lot of time looking for/at objects in them; the accesses to
the packfiles are now optimized by checking the most-recently-used
packfile first.
* jk/pack-objects-optim-mru:
pack-objects: use mru list when iterating over packs
pack-objects: break delta cycles before delta-search phase
sha1_file: make packed_object_info public
provide an initializer for "struct object_info"
We call "qsort(array, nelem, sizeof(array[0]), fn)", and most of
the time third parameter is redundant. A new QSORT() macro lets us
omit it.
* rs/qsort:
show-branch: use QSORT
use QSORT, part 2
coccicheck: use --all-includes by default
remove unnecessary check before QSORT
use QSORT
add QSORT
Code clean-up with help from coccinelle tool continues.
* rs/cocci:
coccicheck: make transformation for strbuf_addf(sb, "...") more precise
use strbuf_add_unique_abbrev() for adding short hashes, part 2
use strbuf_addstr() instead of strbuf_addf() with "%s", part 2
gitignore: ignore output files of coccicheck make target
In recent versions of cURL, GSSAPI credential delegation is
disabled by default due to CVE-2011-2192; introduce a configuration
to selectively allow enabling this.
* ps/http-gssapi-cred-delegation:
http: control GSSAPI credential delegation
The "graph" API used in "git log --graph" miscounted the number of
output columns consumed so far when drawing a padding line, which
has been fixed; this did not affect any existing code as nobody
tried to write anything after the padding on such a line, though.
* jk/graph-padding-fix:
graph: fix extra spaces in graph_padding_line
Almost everybody uses DEFAULT_ABBREV to refer to the default
setting for the abbreviation, but "git blame" peeked into
underlying variable bypassing the macro for no good reason.
* jc/blame-abbrev:
blame: use DEFAULT_ABBREV macro
"git log rev^..rev" is an often-used revision range specification
to show what was done on a side branch merged at rev. This has
gained a short-hand "rev^-1". In general "rev^-$n" is the same as
"^rev^$n rev", i.e. what has happened on other branches while the
history leading to nth parent was looking the other way.
* vn/revision-shorthand-for-side-branch-log:
revision: new rev^-n shorthand for rev^n..rev
When given an abbreviated object name that is not (or more
realistically, "no longer") unique, we gave a fatal error
"ambiguous argument". This error is now accompanied by hints that
lists the objects that begins with the given prefix. During the
course of development of this new feature, numerous minor bugs were
uncovered and corrected, the most notable one of which is that we
gave "short SHA1 xxxx is ambiguous." twice without good reason.
* jk/ambiguous-short-object-names:
get_short_sha1: make default disambiguation configurable
get_short_sha1: list ambiguous objects on error
for_each_abbrev: drop duplicate objects
sha1_array: let callbacks interrupt iteration
get_short_sha1: mark ambiguity error for translation
get_short_sha1: NUL-terminate hex prefix
get_short_sha1: refactor init of disambiguation code
get_short_sha1: parse tags when looking for treeish
get_sha1: propagate flags to child functions
get_sha1: avoid repeating ourselves via ONLY_TO_DIE
get_sha1: detect buggy calls with multiple disambiguators
An author name, that spelled a backslash-quoted double quote in the
human readable part "My \"double quoted\" name", was not unquoted
correctly while applying a patch from a piece of e-mail.
* kd/mailinfo-quoted-string:
mailinfo: unescape quoted-pair in header fields
t5100-mailinfo: replace common path prefix with variable
The original command line syntax for "git merge", which was "git
merge <msg> HEAD <parent>...", has been deprecated for quite some
time, and "git gui" was the last in-tree user of the syntax. This
is finally fixed, so that we can move forward with the deprecation.
* rs/git-gui-use-modern-git-merge-syntax:
git-gui: stop using deprecated merge syntax
Codepaths that read from an on-disk loose object were too loose in
validating what they are reading is a proper object file and
sometimes read past the data they read from the disk, which has
been corrected. H/t to Gustavo Grieco for reporting.
* jc/verify-loose-object-header:
unpack_sha1_header(): detect malformed object header
streaming: make sure to notice corrupt object
"git init" tried to record core.worktree in the repository's
'config' file when GIT_WORK_TREE environment variable was set and
it was different from where GIT_DIR appears as ".git" at its top,
but the logic was faulty when .git is a "gitdir:" file that points
at the real place, causing trouble in working trees that are
managed by "git worktree". This has been corrected.
* nd/init-core-worktree-in-multi-worktree-world:
init: kill git_link variable
init: do not set unnecessary core.worktree
init: kill set_git_dir_init()
init: call set_git_dir_init() from within init_db()
init: correct re-initialization from a linked worktree
"gitweb" can spawn "highlight" to show blob contents with
(programming) language-specific syntax highlighting, but only
when the language is known. "highlight" can however be told
to make the guess itself by giving it "--force" option, which
has been enabled.
Merge branch 'jk/ident-ai-canonname-could-be-null' into maint
In the codepath that comes up with the hostname to be used in an
e-mail when the user didn't tell us, we looked at ai_canonname
field in struct addrinfo without making sure it is not NULL first.
"git pack-objects --include-tag" was taught that when we know that
we are sending an object C, we want a tag B that directly points at
C but also a tag A that points at the tag B. We used to miss the
intermediate tag B in some cases.
* jk/pack-tag-of-tag:
pack-objects: walk tag chains for --include-tag
t5305: simplify packname handling
t5305: use "git -C"
t5305: drop "dry-run" of unpack-objects
t5305: move cleanup into test block
ref-filter: strip format option after a field name only once while parsing
When parse_ref_filter_atom() iterates over a list of valid atoms to
check that a field name is one of them, it has to strip the optional
colon-separated format option suffix that might follow the field name.
However, it does so inside the loop, i.e. it performs the exact same
stripping over and over again.
Move stripping the format option suffix out of that loop, so it's only
performed once for each parsed field name.
Signed-off-by: SZEDER Gábor <szeder@ira.uka.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Shorten the code by using QSORT instead of calling qsort(3) directly,
as the former determines the element size automatically and checks if
there are at least two elements to sort already.
Signed-off-by: Rene Scharfe <l.s.r@web.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
coccicheck: make transformation for strbuf_addf(sb, "...") more precise
We can replace strbuf_addf() calls that just add a simple string with
calls to strbuf_addstr() to make the intent clearer. We need to be
careful if that string contains printf format specifications like %%,
though, as a simple replacement would change the output.
Add checks to the semantic patch to make sure we only perform the
transformation if the second argument is a string constant (possibly
translated) that doesn't contain any percent signs.
Signed-off-by: Rene Scharfe <l.s.r@web.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
pretty: avoid adding reset for %C(auto) if output is empty
We emit an escape sequence for resetting color and attribute for
%C(auto) to make sure automatic coloring is displayed as intended.
Stop doing that if the output strbuf is empty, i.e. when %C(auto)
appears at the start of the format string, because then there is no
need for a reset and we save a few bytes in the output.
Signed-off-by: Rene Scharfe <l.s.r@web.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Add a make variable, SPATCH_FLAGS, for specifying flags for spatch, and
set it to --all-includes by default. This option lets it consider
header files which would otherwise be ignored. That's important for
some rules that rely on type information. It doubles the duration of
coccicheck, however.
Signed-off-by: Rene Scharfe <l.s.r@web.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Delegation of credentials is disabled by default in libcurl since
version 7.21.7 due to security vulnerability CVE-2011-2192. Which
makes troubles with GSS/kerberos authentication when delegation
of credentials is required. This can be changed with option
CURLOPT_GSSAPI_DELEGATION in libcurl with set expected parameter
since libcurl version 7.22.0.
This patch provides new configuration variable http.delegation
which corresponds to curl parameter "--delegation" (see man 1 curl).
The following values are supported:
* none (default).
* policy
* always
Signed-off-by: Petr Stodulka <pstodulk@redhat.com> Signed-off-by: Junio C Hamano <gitster@pobox.com>
"git worktree", even though it used the default_abbrev setting that
ought to be affected by core.abbrev configuration variable, ignored
the variable setting. The command has been taught to read the
default set of configuration variables to correct this.
In the codepath that comes up with the hostname to be used in an
e-mail when the user didn't tell us, we looked at ai_canonname
field in struct addrinfo without making sure it is not NULL first.
When "git fetch" tries to find where the history of the repository
it runs in has diverged from what the other side has, it has a
mechanism to avoid digging too deep into irrelevant side branches.
This however did not work well over the "smart-http" transport due
to a design bug, which has been fixed.
* jt/fetch-pack-in-vain-count-with-stateless:
fetch-pack: do not reset in_vain on non-novel acks
A low-level function verify_packfile() was meant to show errors
that were detected without dying itself, but under some conditions
it didn't and died instead, which has been fixed.
* jk/verify-packfile-gently:
verify_packfile: check pack validity before accessing data
When "git format-patch --stdout" output is placed as an in-body
header and it uses the RFC2822 header folding, "git am" failed to
put the header line back into a single logical line. The
underlying "git mailinfo" was taught to handle this properly.
* jt/mailinfo-fold-in-body-headers:
mailinfo: handle in-body header continuations
mailinfo: make is_scissors_line take plain char *
mailinfo: separate in-body header processing
"git add --chmod=+x <pathspec>" added recently only toggled the
executable bit for paths that are either new or modified. This has
been corrected to flip the executable bit for all paths that match
the given pathspec.
* tg/add-chmod+x-fix:
t3700-add: do not check working tree file mode without POSIXPERM
t3700-add: create subdirectory gently
add: modify already added files when --chmod is given
read-cache: introduce chmod_index_entry
update-index: add test for chmod flags
Merge branch 'rt/rebase-i-broken-insn-advise' into maint
When "git rebase -i" is given a broken instruction, it told the
user to fix it with "--edit-todo", but didn't say what the step
after that was (i.e. "--continue").
* rt/rebase-i-broken-insn-advise:
rebase -i: improve advice on bad instruction lines
Merge branch 'ls/travis-homebrew-path-fix' into maint
The procedure to build Git on Mac OS X for Travis CI hardcoded the
internal directory structure we assumed HomeBrew uses, which was a
no-no. The procedure has been updated to ask HomeBrew things we
need to know to fix this.
* ls/travis-homebrew-path-fix:
travis-ci: ask homebrew for its path instead of hardcoding it
Some codepaths in "git diff" used regexec(3) on a buffer that was
mmap(2)ed, which may not have a terminating NUL, leading to a read
beyond the end of the mapped region. This was fixed by introducing
a regexec_buf() helper that takes a <ptr,len> pair with REG_STARTEND
extension.
* js/regexec-buf:
regex: use regexec_buf()
regex: add regexec_buf() that can work on a non NUL-terminated string
regex: -G<pattern> feeds a non NUL-terminated string to regexec() and fails
Merge branch 'nd/checkout-disambiguation' into maint
"git checkout <word>" does not follow the usual disambiguation
rules when the <word> can be both a rev and a path, to allow
checking out a branch 'foo' in a project that happens to have a
file 'foo' in the working tree without having to disambiguate.
This was poorly documented and the check was incorrect when the
command was run from a subdirectory.
* nd/checkout-disambiguation:
checkout: fix ambiguity check in subdir
checkout.txt: document a common case that ignores ambiguation rules
checkout: add some spaces between code and comment
Merge branch 'mm/config-color-ui-default-to-auto' into maint
Documentation for individual configuration variables to control use
of color (like `color.grep`) said that their default value is
'false', instead of saying their default is taken from `color.ui`.
When we updated the default value for color.ui from 'false' to
'auto' quite a while ago, all of them broke. This has been
corrected.
* mm/config-color-ui-default-to-auto:
Documentation/config: default for color.* is color.ui
Merge branch 'jk/reduce-gc-aggressive-depth' into maint
"git gc --aggressive" used to limit the delta-chain length to 250,
which is way too deep for gaining additional space savings and is
detrimental for runtime performance. The limit has been reduced to
50.
* jk/reduce-gc-aggressive-depth:
gc: default aggressive depth to 50
Merge branch 'jk/rebase-i-drop-ident-check' into maint
Even when "git pull --rebase=preserve" (and the underlying "git
rebase --preserve") can complete without creating any new commit
(i.e. fast-forwards), it still insisted on having a usable ident
information (read: user.email is set correctly), which was less
than nice. As the underlying commands used inside "git rebase"
would fail with a more meaningful error message and advice text
when the bogus ident matters, this extra check was removed.
* jk/rebase-i-drop-ident-check:
rebase-interactive: drop early check for valid ident
Merge branch 'jt/format-patch-base-info-above-sig' into maint
"git format-patch --base=..." feature that was recently added
showed the base commit information after "-- " e-mail signature
line, which turned out to be inconvenient. The base information
has been moved above the signature line.
* jt/format-patch-base-info-above-sig:
format-patch: show base info before email signature
Merge branch 'rs/xdiff-merge-overlapping-hunks-for-W-context' into maint
"git diff -W" output needs to extend the context backward to
include the header line of the current function and also forward to
include the body of the entire current function up to the header
line of the next one. This process may have to merge to adjacent
hunks, but the code forgot to do so in some cases.
* rs/xdiff-merge-overlapping-hunks-for-W-context:
xdiff: fix merging of hunks with -W context and -u context
Merge branch 'ew/http-do-not-forget-to-call-curl-multi-remove-handle' into maint
The http transport (with curl-multi option, which is the default
these days) failed to remove curl-easy handle from a curlm session,
which led to unnecessary API failures.
* ew/http-do-not-forget-to-call-curl-multi-remove-handle:
http: always remove curl easy from curlm session on release
http: consolidate #ifdefs for curl_multi_remove_handle
http: warn on curl_multi_add_handle failures
"git log --cherry-pick" used to include merge commits as candidates
to be matched up with other commits, resulting a lot of wasted time.
The patch-id generation logic has been updated to ignore merges to
avoid the wastage.
* jk/patch-ids-no-merges:
patch-ids: refuse to compute patch-id for merge commit
patch-ids: turn off rename detection
Merge branch 'js/git-gui-commit-gpgsign' into maint
"git commit-tree" stopped reading commit.gpgsign configuration
variable that was meant for Porcelain "git commit" in Git 2.9; we
forgot to update "git gui" to look at the configuration to match
this change.
* js/git-gui-commit-gpgsign:
git-gui: respect commit.gpgsign again
* sy/git-gui-i18n-ja:
git-gui: update Japanese information
git-gui: update Japanese translation
git-gui: add Japanese language code
git-gui: apply po template to Japanese translation
git-gui: consistently use the same word for "blame" in Japanese
git-gui: consistently use the same word for "remote" in Japanese
The graph_padding_line() function outputs a series of "|"
columns, and then pads with spaces to graph->width by
calling graph_pad_horizontally(). However, we tell the
latter that we wrote graph->num_columns characters, which is
not true; we also needed spaces between the columns. Let's
keep a count of how many characters we've written, which is
what all the other callers of graph_pad_horizontally() do.
Without this, any output that is written at the end of a
padding line will be bumped out by at least an extra
graph->num_columns spaces. Presumably nobody ever noticed
the bug because there's no code path that actually writes to
the end of a padding line.
Signed-off-by: Jeff King <peff@peff.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Apply the semantic patch contrib/coccinelle/qsort.cocci to the code
base, replacing calls of qsort(3) with QSORT. The resulting code is
shorter and supports empty arrays with NULL pointers.
Signed-off-by: Rene Scharfe <l.s.r@web.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Add the macro QSORT, a convenient wrapper for qsort(3) that infers the
size of the array elements and supports the convention of initializing
empty arrays with a NULL pointer, which we use in some places.
Calling qsort(3) directly with a NULL pointer is undefined -- even with
an element count of zero -- and allows the compiler to optimize away any
following NULL checks. Using the macro avoids such surprises.
Add a semantic patch as well to demonstrate the macro's usage and to
automate the transformation of trivial cases.
Signed-off-by: Rene Scharfe <l.s.r@web.de> Signed-off-by: Junio C Hamano <gitster@pobox.com>
This does not make any practical difference in today's code, but
everybody else accesses the default abbreviation length via the
DEFAULT_ABBREV macro. Make sure this oddball codepath does not
stray from the convention.
t5100-mailinfo: replace common path prefix with variable
Many tests need to store data in a file, and repeat the same pattern to
refer to that path:
"$TEST_DIRECTORY"/t5100/
Create a variable that contains this path, and use that instead.
While we're making this change, make sure the quotes are not just around
the variable, but around the entire string to not give the impression
we want shell splitting to affect the other variables.
Signed-off-by: Kevin Daudt <me@ikke.info> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Users often wonder if the oldest or the newest n commits are shown
by `log -n --reverse`. Clarify that --reverse kicks in only after
deciding which commits are to be shown to unconfuse them.
Reported-by: Ruediger Meier <sweet_f_a@gmx.de> Signed-off-by: Pranit Bauva <pranit.bauva@gmail.com> Signed-off-by: Junio C Hamano <gitster@pobox.com>
tree-walk: be more specific about corrupt tree errors
When the tree-walker runs into an error, it just calls
die(), and the message is always "corrupt tree file".
However, we are actually covering several cases here; let's
give the user a hint about what happened.
Let's also avoid using the word "corrupt", which makes it
seem like the data bit-rotted on disk. Our sha1 check would
already have found that. These errors are ones of data that
is malformed in the first place.
Signed-off-by: David Turner <dturner@twosigma.com> Signed-off-by: Jeff King <peff@peff.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
use strbuf_add_unique_abbrev() for adding short hashes, part 2
Call strbuf_add_unique_abbrev() to add abbreviated hashes to strbufs
instead of taking detours through find_unique_abbrev() and its static
buffer. This is shorter and a bit more efficient.
"git log rev^..rev" is commonly used to show all work done on and merged
from a side branch. This patch introduces a shorthand "rev^-" for this
and additionally allows "rev^-$n" to mean "reachable from rev, excluding
what is reachable from the nth parent of rev". For example, for a
two-parent merge, you can use rev^-2 to get the set of commits which were
made to the main branch while the topic branch was prepared.
Signed-off-by: Vegard Nossum <vegard.nossum@oracle.com> Signed-off-by: Junio C Hamano <gitster@pobox.com>
The command accesses default_abbrev (defined in environment.c and is
updated via core.abbrev configuration), but never makes any call to
git_config(). The output from "worktree list" ignores the abbrev
setting for this reason.
Make a call to git_config() to read the default set of configuration
variables at the beginning of the command.
get_short_sha1: make default disambiguation configurable
When we find ambiguous short sha1s, we may get a
disambiguation rule from our caller's context. But if we
don't, we fall back to treating all sha1s the same, even
though most projects will tend to refer only to commits by
their short sha1s.
This patch introduces a configuration option that lets the
user pick a different fallback (e.g., only commits). It's
possible that we may want to make this the default, but it's
a good idea to start as a config option for two reasons:
1. It lets people experiment with this and see if it's a
good idea (i.e., the "tend to" above is an assumption;
we don't really know if this will break some obscure
cases).
2. Even if we do flip the default, it gives people an
escape hatch if it causes problems (you can sometimes
override it by asking for "1234^{tree}", but not all
combinations are possible).
Signed-off-by: Jeff King <peff@peff.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
Commit e8adf23 (xdl_change_compact(): introduce the concept
of a change group, 2016-08-22) added a "struct group" type
to xdiff/xdiffi.c. But the POSIX system header "grp.h"
already defines "struct group" (it is part of the getgrnam
interface). This happens to work because the new type is
local to xdiffi.c, and the xdiff code includes a relatively
small set of system headers. But it will break compilation
if xdiff ever switches to using git-compat-util.h. It can
also probably cause confusion with tools that look at the
whole code base, like coccinelle or ctags.
Let's resolve by giving the xdiff variant a scoped name,
which is closer to other xdiff types anyway (e.g.,
xdlfile_t, though note that xdiff is fond if typedefs when
Git usually is not).
Signed-off-by: Jeff King <peff@peff.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>
When "git rebase -i" is given a broken instruction, it told the
user to fix it with "--edit-todo", but didn't say what the step
after that was (i.e. "--continue").
* rt/rebase-i-broken-insn-advise:
rebase -i: improve advice on bad instruction lines
The procedure to build Git on Mac OS X for Travis CI hardcoded the
internal directory structure we assumed HomeBrew uses, which was a
no-no. The procedure has been updated to ask HomeBrew things we
need to know to fix this.
* ls/travis-homebrew-path-fix:
travis-ci: ask homebrew for its path instead of hardcoding it
"git add --chmod=+x <pathspec>" added recently only toggled the
executable bit for paths that are either new or modified. This has
been corrected to flip the executable bit for all paths that match
the given pathspec.
* tg/add-chmod+x-fix:
t3700-add: do not check working tree file mode without POSIXPERM
t3700-add: create subdirectory gently
add: modify already added files when --chmod is given
read-cache: introduce chmod_index_entry
update-index: add test for chmod flags