When running "git add --refresh <pathspec>", we incorrectly showed the
path that is unmerged even if it is outside the specified pathspec, even
though we did honor pathspec and refreshed only the paths that matched.

Note that this cange does not affect "git update-index --refresh"; for
hysterical raisins, it does not take a pathspec (it takes real paths) and
more importantly itss command line options are parsed and executed one by
one as they are encountered, so "git update-index --refresh foo" means
"first refresh the index, and then update the entry 'foo' by hashing the
contents in file 'foo'", not "refresh only entry 'foo'".
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

If you have a deleted file and a porcelain refreshes the
cache, we print:

  Unstaged changes after reset:
  M	file

This is technically correct, in that the file is modified,
but it's friendlier to the user if we further differentiate
the case of a deleted file (especially because this output
looks a lot like "diff --name-status", which would also make
the distinction).

Similarly, we can distinguish typechanges ("T") and
intent-to-add files ("A"), both of which appear as just "M"
in the current output.

The plumbing output for all cases remains "needs update" for
historical compatibility.
Signed-off-by: NJeff King <peff@peff.net>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

When refreshing the index, for modified (or unmerged) files we will print
"needs update" (or "needs merge") for plumbing, or line similar to the
output from "diff --name-status" for porcelain.

The variables holding which type of message to show are named after the
plumbing messages. However, as we begin to differentiate more cases at the
porcelain level (with the plumbing message staying the same), that naming
scheme will become awkward.

Instead, name the variables after which case we found (modified or
unmerged), not what we will output.
Signed-off-by: NJeff King <peff@peff.net>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

This will enable refresh_cache to differentiate more cases
of modification (such as typechange) when telling the user
what isn't fresh.
Signed-off-by: NJeff King <peff@peff.net>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

The code to estimate the in-memory size of the index based on its on-disk
representation is subtly wrong for certain architecture-dependent struct
layouts.  Instead of fixing it, replace the code to keep the index entries
in a single large block of memory and allocate each entry separately
instead.  This is both simpler and more flexible, as individual entries
can now be freed.  Actually using that added flexibility is left for a
later patch.
Suggested-by: NJunio C Hamano <gitster@pobox.com>
Signed-off-by: NRene Scharfe <rene.scharfe@lsrfire.ath.cx>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

estimate_cache_size() tries to guess how much memory is needed for the
in-memory representation of an index file.  It does that by using the
file size, the number of entries and the difference of the sizes of the
on-disk and in-memory structs -- without having to check the length of
the name of each entry, which varies for each entry, but their sums are
the same no matter the representation.

Except there can be a difference.  First of all, the size is really
calculated by ce_size and ondisk_ce_size based on offsetof(..., name),
not sizeof, which can be different.  And entries are padded with 1 to 8
NULs at the end (after the variable name) to make their total length a
multiple of eight.

So in order to allocate enough memory to hold the index, change the
delta calculation to be based on offsetof(..., name) and round up to
the next multiple of eight.

On a 32-bit Linux, this delta was used before:

	sizeof(struct cache_entry)        == 72
	sizeof(struct ondisk_cache_entry) == 64
	                                    ---
	                                      8

The actual difference for an entry with a filename length of one was,
however (find the definitions are in cache.h):

	offsetof(struct cache_entry, name)        == 72
	offsetof(struct ondisk_cache_entry, name) == 62

	ce_size        == (72 + 1 + 8) & ~7 == 80
	ondisk_ce_size == (62 + 1 + 8) & ~7 == 64
	                                      ---
	                                       16

So eight bytes less had been allocated for such entries.  The new
formula yields the correct delta:

	(72 - 62 + 7) & ~7 == 16
Reported-by: NJohn Hsing <tsyj2007@gmail.com>
Signed-off-by: NRene Scharfe <rene.scharfe@lsrfire.ath.cx>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

I've deliberately excluded the borrowed code in compat/nedmalloc
directory.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

verify_dotfile() currently assumes that the path seperator is '/', but on
Windows it can also be '\\', so use is_dir_sep() instead.
Signed-off-by: NTheo Niessink <theo@taletn.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

We simply want to say "At a directory boundary, be careful with a name
that begins with a dot, forbid a name that ends with the boundary
character or has duplicated bounadry characters".
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

If someone manage to create a repo with a 'C:' entry in the
root-tree, files can be written outside of the working-dir. This
opens up a can-of-worms of exploits.

Fix it by explicitly checking for a dos drive prefix when verifying
a paht. While we're at it, make sure that paths beginning with '\' is
considered absolute as well.
Noticed-by: NTheo Niessink <theo@taletn.com>
Signed-off-by: NErik Faye-Lund <kusmabite@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

The "format_check" parameter tucked after the existing parameters is too
ugly an afterthought to live in any reasonable API.

Combine it with the other boolean parameter "write_object" into a single
"flags" parameter.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Traditional "opportunistic index update" done by read-only "diff" and
"status" was about updating cached lstat(2) information in the index for
the next round.  We missed another obvious optimization opportunity: when
there are racily clean entries that will cease to be racily clean by
updating $GIT_INDEX_FILE.  Detect that case and write $GIT_INDEX_FILE out
to give it a newer timestamp.

Noticed by Lasse Makholm by stracing "git status" in a fresh checkout and
counting the number of open(2) calls.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

When we had to refresh the index internally before running diff or status,
we opportunistically updated the $GIT_INDEX_FILE so that later invocation
of git can use the lstat(2) we already did in this invocation.

Make them share a helper function to do so.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Signed-off-by: NJonathan Nieder <jrnieder@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Commits, trees and tags have structure. Don't let users feed git
with malformed ones. Sooner or later git will die() when
encountering them.

Note that this patch does not check semantics. A tree that points
to non-existent objects is perfectly OK (and should be so, users
may choose to add commit first, then its associated tree for example).
Signed-off-by: NNguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Signed-off-by: NNguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Signed-off-by: NNguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

When MyDir/ABC/filea.txt is added to Git, the disk directory MyDir/ABC/
is renamed to mydir/aBc/, and then mydir/aBc/fileb.txt is added, the
index will contain MyDir/ABC/filea.txt and mydir/aBc/fileb.txt. Although
the earlier portions of this patch series account for those differences
in case, this patch makes the pathing consistent by folding the case of
newly added files against the first file added with that path.

In read-cache.c's add_to_index(), the index_name_exists() support used
for git status's case insensitive directory lookups is used to find the
proper directory case according to what the user already checked in.
That is, MyDir/ABC/'s case is used to alter the stored path for
fileb.txt to MyDir/ABC/fileb.txt (instead of mydir/aBc/fileb.txt).

This is especially important when cloning a repository to a case
sensitive file system. MyDir/ABC/ and mydir/aBc/ exist in the same
directory on a Windows machine, but on Linux, the files exist in two
separate directories. The update to add_to_index(), in effect, treats a
Windows file system as case sensitive by making path case consistent.
Signed-off-by: NJoshua Jensen <jjensen@workspacewhiz.com>
Signed-off-by: NJohannes Sixt <j6t@kdbg.org>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Noticed with valgrind.
Signed-off-by: NJonathan Nieder <jrnieder@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

The new dircache extension CACHE_EXT_RESOLVE_UNDO, whose value is
0x52455543, is actually the ASCII sequence 'REUC', not the ASCII
sequence 'REUN'.
Signed-off-by: NShawn O. Pearce <spearce@spearce.org>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

The rule has always been that a cache entry that is ce_uptodate(ce)
means that we already have checked the work tree entity and we know
there is no change in the work tree compared to the index, and nobody
should have to double check.  Note that false ce_uptodate(ce) does not
mean it is known to be dirty---it only means we don't know if it is
clean.

There are a few codepaths (refresh-index and preload-index are among
them) that mark a cache entry as up-to-date based solely on the return
value from ie_match_stat(); this function uses lstat() to see if the
work tree entity has been touched, and for a submodule entry, if its
HEAD points at the same commit as the commit recorded in the index of
the superproject (a submodule that is not even cloned is considered
clean).

A submodule is no longer considered unmodified merely because its HEAD
matches the index of the superproject these days, in order to prevent
people from forgetting to commit in the submodule and updating the
superproject index with the new submodule commit, before commiting the
state in the superproject.  However, the patch to do so didn't update
the codepath that marks cache entries up-to-date based on the updated
definition and instead worked it around by saying "we don't trust the
return value of ce_uptodate() for submodules."

This makes ce_uptodate() trustworthy again by not marking submodule
entries up-to-date.

The next step _could_ be to introduce a few "in-core" flag bits to
cache_entry structure to record "this entry is _known_ to be dirty",
call is_submodule_modified() from ie_match_stat(), and use these new
bits to avoid running this rather expensive check more than once, but
that can be a separate patch.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Exal Sibeaz pointed out that some git files are way too big, and that
add_files_to_cache() brings in all the diff machinery to any git binary
that needs the basic git SHA1 object operations from read-cache.c. Which
is pretty much all of them.

It's doubly silly, since add_files_to_cache() is only used by builtin
programs (add, checkout and commit), so it's fairly easily fixed by just
moving the thing to builtin-add.c, and avoiding the dependency entirely.

I initially argued to Exal that it would probably be best to try to depend
on smart compilers and linkers, but after spending some time trying to
make -ffunction-sections work and giving up, I think Exal was right, and
the fix is to just do some trivial cleanups like this.

This trivial cleanup results in pretty stunning file size differences.
The diff machinery really is mostly used by just the builtin programs, and
you have things like these trivial before-and-after numbers:

  -rwxr-xr-x 1 torvalds torvalds 1727420 2010-01-21 10:53 git-hash-object
  -rwxrwxr-x 1 torvalds torvalds  940265 2010-01-21 11:16 git-hash-object

Now, I'm not saying that 940kB is good either, but that's mostly all the
debug information - you can see the real code with 'size':

   text	   data	    bss	    dec	    hex	filename
 418675	   3920	 127408	 550003	  86473	git-hash-object (before)
 230650	   2288	 111728	 344666	  5425a	git-hash-object (after)

ie we have a nice 24% size reduction from this trivial cleanup.

It's not just that one file either. I get:

	[torvalds@nehalem git]$ du -s /home/torvalds/libexec/git-core
	45640	/home/torvalds/libexec/git-core (before)
	33508	/home/torvalds/libexec/git-core (after)

so we're talking 12MB of diskspace here.

(Of course, stripping all the binaries brings the 33MB down to 9MB, so the
whole debug information thing is still the bulk of it all, but that's a
separate issue entirely)

Now, I'm sure there are other things we should do, and changing our
compiler flags from -O2 to -Os would bring the text size down by an
additional almost 20%, but this thing Exal pointed out seems to be some
good low-hanging fruit.
Signed-off-by: NLinus Torvalds <torvalds@linux-foundation.org>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

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

Commit 9e8eceab (Add 'merge' mode to 'git reset', 2008-12-01) disallowed
"git reset --merge" when there was unmerged entries.  But it wished if
unmerged entries were reset as if --hard (instead of --merge) has been
used.  This makes sense because all "mergy" operations makes sure that
any path involved in the merge does not have local modifications before
starting, so resetting such a path away won't lose any information.

The previous commit changed the behavior of --merge to accept resetting
unmerged entries if they are reset to a different state than HEAD, but it
did not reset the changes in the work tree, leaving the conflict markers
in the resulting file in the work tree.

Fix it by doing three things:

 - Update the documentation to match the wish of original "reset --merge"
   better, namely, "An unmerged entry is a sign that the path didn't have
   any local modification and can be safely resetted to whatever the new
   HEAD records";

 - Update read_index_unmerged(), which reads the index file into the cache
   while dropping any higher-stage entries down to stage #0, not to copy
   the object name from the higher stage entry.  The code used to take the
   object name from the a stage entry ("base" if you happened to have
   stage #1, or "ours" if both sides added, etc.), which essentially meant
   that you are getting random results depending on what the merge did.

   The _only_ reason we want to keep a previously unmerged entry in the
   index at stage #0 is so that we don't forget the fact that we have
   corresponding file in the work tree in order to be able to remove it
   when the tree we are resetting to does not have the path.  In order to
   differentiate such an entry from ordinary cache entry, the cache entry
   added by read_index_unmerged() is marked as CE_CONFLICTED.

 - Update merged_entry() and deleted_entry() so that they pay attention to
   cache entries marked as CE_CONFLICTED.  They are previously unmerged
   entries, and the files in the work tree that correspond to them are
   resetted away by oneway_merge() to the version from the tree we are
   resetting to.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

On big endian platforms with 8-byte unsigned long, the code reads the
size of the index extension section (which is a 4-byte network byte
order integer) incorrectly.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

When resolving a conflict using "git add" to create a stage #0 entry, or
"git rm" to remove entries at higher stages, remove_index_entry_at()
function is eventually called to remove unmerged (i.e. higher stage)
entries from the index.  Introduce a "resolve_undo_info" structure and
keep track of the removed cache entries, and save it in a new index
extension section in the index_state.

Operations like "read-tree -m", "merge", "checkout [-m] <branch>" and
"reset" are signs that recorded information in the index is no longer
necessary.  The data is removed from the index extension when operations
start; they may leave conflicted entries in the index, and later user
actions like "git add" will record their conflicted states afresh.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Previously CE_MATCH_IGNORE_VALID flag is used by both valid and
skip-worktree bits. While the two bits have similar behaviour, sharing
this flag means "git update-index --really-refresh" will ignore
skip-worktree while it should not. Instead another flag is
introduced to ignore skip-worktree bit, CE_MATCH_IGNORE_VALID only
applies to valid bit.
Signed-off-by: NNguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

grep: turn on --cached for files that is marked skip-worktree
ls-files: do not check for deleted file that is marked skip-worktree
update-index: ignore update request if it's skip-worktree, while still allows removing
diff*: skip worktree version
Signed-off-by: NNguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

git reset without argument displays a summary of the local modification,
like this:

    $ git reset
    Makefile: locally modified

Some people have problems with this; they look like an error message.

This patch makes its output mimic how "git checkout $another_branch"
reports the paths with local modifications.  "git add --refresh --verbose"
is changed in the same way.

It also adds a header to make it clear that the output is informative,
and not an error.
Signed-off-by: NMatthieu Moy <Matthieu.Moy@imag.fr>

The change in the output is going to become more general than just saying
"changed", so let's make the variable name more general too.
Signed-off-by: NMatthieu Moy <Matthieu.Moy@imag.fr>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Lots of die() calls did not actually report the kind of error, which
can leave the user confused as to the real problem.  Use die_errno()
where we check a system/library call that sets errno on failure, or
one of the following that wrap such calls:

  Function              Passes on error from
  --------              --------------------
  odb_pack_keep         open
  read_ancestry         fopen
  read_in_full          xread
  strbuf_read           xread
  strbuf_read_file      open or strbuf_read_file
  strbuf_readlink       readlink
  write_in_full         xwrite
Signed-off-by: NThomas Rast <trast@student.ethz.ch>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Change calls to die(..., strerror(errno)) to use the new die_errno().

In the process, also make slight style adjustments: at least state
_something_ about the function that failed (instead of just printing
the pathname), and put paths in single quotes.
Signed-off-by: NThomas Rast <trast@student.ethz.ch>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Commit e1afca4f "write_index(): update index_state->timestamp after
flushing to disk" on 2009-02-23 used stat.ctime to record the
timestamp of the index-file.  This is wrong, so fix this and use the
correct stat.mtime timestamp instead.

Commit 110c46a9 "Not all systems use st_[cm]tim field for ns
resolution file timestamp" on 2009-03-08, has a similar bug for the
builtin-fetch-pack.c file.
Signed-off-by: NKjetil Barvik <barvik@broadpark.no>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Some codepaths do not still use the ST_[CM]TIME_NSEC() pair of macros
introduced by the previous commit but assumes all systems use st_mtim
and st_ctim fields in "struct stat" to record nanosecond resolution part
of the file timestamps.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Traditionally, the lack of USE_NSEC meant "do not record nor use the
nanosecond resolution part of the file timestamps".  To avoid problems on
filesystems that lose the ns part when the metadata is flushed to the disk
and then later read back in, disabling USE_NSEC has been a good idea in
general.

If you are on a filesystem without such an issue, it does not hurt to read
and store them in the cached stat data in the index entries even if your
git is compiled without USE_NSEC.  The index left with such a version of
git can be read by git compiled with USE_NSEC and it can make use of the
nanosecond part to optimize the check to see if the path on the filesystem
hsa been modified since we last looked at.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Since this timestamp is used to check for racy-clean files, it is
important to keep it uptodate.

For the 'git checkout' command without the '-q' option, this make a
huge difference.  Before, each and every file which was updated, was
racy-clean after the call to unpack_trees() and write_index() but
before the GIT process ended.

And because of the call to show_local_changes() in builtin-checkout.c,
we ended up reading those files back into memory, doing a SHA1 to
check if the files was really different from the index.  And, of
course, no file was different.

With this fix, 'git checkout' without the '-q' option should now be
almost as fast as with the '-q' option, but not quite, as we still do
some few lstat(2) calls more without the '-q' option.

Below is some average numbers for 10 checkout's to v2.6.27 and 10 to
v2.6.25 of the Linux kernel, to show the difference:

before (git version 1.6.2.rc1.256.g58a87):
 7.860 user  2.427 sys  19.465 real  52.8% CPU  faults: 0 major 95331 minor
after:
 6.184 user  2.160 sys  17.619 real  47.4% CPU  faults: 0 major 38994 minor
Signed-off-by: NKjetil Barvik <barvik@broadpark.no>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Since the filesystem ext4 is now defined as stable in Linux v2.6.28,
and ext4 supports nanonsecond resolution timestamps natively, it is
time to make USE_NSEC work as expected.

This will make racy git situations less likely to happen.  For 'git
checkout' this means it will be less likely that we have to open, read
the contents of the file into RAM, and check if file is really
modified or not.  The result sould be a litle less used CPU time, less
pagefaults and a litle faster program, at least for 'git checkout'.

Since the number of possible racy git situations would increase when
disks gets faster, this patch would be more and more helpfull as times
go by.  For a fast Solid State Disk, this patch should be helpfull.

Note that, when file operations starts to take less than 1 nanosecond,
one would again start to get more racy git situations.

For more info on racy git, see Documentation/technical/racy-git.txt
For more info on ext4, see http://kernelnewbies.org/Ext4Signed-off-by: NKjetil Barvik <barvik@broadpark.no>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

Below is oprofile output from GIT command 'git chekcout -q my-v2.6.25'
(move from tag v2.6.27 to tag v2.6.25 of the Linux kernel):

CPU: Core 2, speed 1999.95 MHz (estimated)
Counted CPU_CLK_UNHALTED events (Clock cycles when not halted) with a unit
                         mask of 0x00 (Unhalted core cycles) count 20000
Counted INST_RETIRED_ANY_P events (number of instructions retired) with a
                           unit mask of 0x00 (No unit mask) count 20000
CPU_CLK_UNHALT...|INST_RETIRED:2...|
  samples|      %|  samples|      %|
------------------------------------
   409247 100.000    342878 100.000 git
        CPU_CLK_UNHALT...|INST_RETIRED:2...|
          samples|      %|  samples|      %|
        ------------------------------------
           260476 63.6476    257843 75.1996 libz.so.1.2.3
           100876 24.6492     64378 18.7758 kernel-2.6.28.4_2.vmlinux
            30850  7.5382      7874  2.2964 libc-2.9.so
            14775  3.6103      8390  2.4469 git
             2020  0.4936      4325  1.2614 libcrypto.so.0.9.8
              191  0.0467        32  0.0093 libpthread-2.9.so
               58  0.0142        36  0.0105 ld-2.9.so
                1 2.4e-04         0       0 libldap-2.3.so.0.2.31

Detail list of the top 20 function entries (libz counted in one blob):

CPU_CLK_UNHALTED  INST_RETIRED_ANY_P
samples  %        samples  %        image name               symbol name
260476   63.6862  257843   75.2725  libz.so.1.2.3            /lib/libz.so.1.2.3
16587     4.0555  3636      1.0615  libc-2.9.so              memcpy
7710      1.8851  277       0.0809  libc-2.9.so              memmove
3679      0.8995  1108      0.3235  kernel-2.6.28.4_2.vmlinux d_validate
3546      0.8670  2607      0.7611  kernel-2.6.28.4_2.vmlinux __getblk
3174      0.7760  1813      0.5293  libc-2.9.so              _int_malloc
2396      0.5858  3681      1.0746  kernel-2.6.28.4_2.vmlinux copy_to_user
2270      0.5550  2528      0.7380  kernel-2.6.28.4_2.vmlinux __link_path_walk
2205      0.5391  1797      0.5246  kernel-2.6.28.4_2.vmlinux ext4_mark_iloc_dirty
2103      0.5142  1203      0.3512  kernel-2.6.28.4_2.vmlinux find_first_zero_bit
2077      0.5078  997       0.2911  kernel-2.6.28.4_2.vmlinux do_get_write_access
2070      0.5061  514       0.1501  git                      cache_name_compare
2043      0.4995  1501      0.4382  kernel-2.6.28.4_2.vmlinux rcu_irq_exit
2022      0.4944  1732      0.5056  kernel-2.6.28.4_2.vmlinux __ext4_get_inode_loc
2020      0.4939  4325      1.2626  libcrypto.so.0.9.8       /usr/lib/libcrypto.so.0.9.8
1965      0.4804  1384      0.4040  git                      patch_delta
1708      0.4176  984       0.2873  kernel-2.6.28.4_2.vmlinux rcu_sched_grace_period
1682      0.4112  727       0.2122  kernel-2.6.28.4_2.vmlinux sysfs_slab_alias
1659      0.4056  290       0.0847  git                      find_pack_entry_one
1480      0.3619  1307      0.3816  kernel-2.6.28.4_2.vmlinux ext4_writepage_trans_blocks

Notice the memmove line, where the CPU did 7710 / 277 = 27.8 cycles
per instruction, and compared to the total cycles spent inside the
source code of GIT for this command, all the memmove() calls
translates to (7710 * 100) / 14775 = 52.2% of this.

Retesting with a GIT program compiled for gcov usage, I found out that
the memmove() calls came from remove_index_entry_at() in read-cache.c,
where we have:

        memmove(istate->cache + pos,
                istate->cache + pos + 1,
                (istate->cache_nr - pos) * sizeof(struct cache_entry *));

remove_index_entry_at() is called 4902 times from check_updates() in
unpack-trees.c, and each time called we move each cache_entry pointers
(from the removed one) one step to the left.

Since we have 28828 entries in the cache this time, and if we on
average move half of them each time, we in total move approximately
4902 * 0.5 * 28828 * 4 = 282 629 712 bytes, or twice this amount if
each pointer is 8 bytes (64 bit).

OK, is seems that the function check_updates() is called 28 times, so
the estimated guess above had been more correct if check_updates() had
been called only once, but the point is: we get lots of bytes moved.

To fix this, and use an O(N) algorithm instead, where N is the number
of cache_entries, we delete/remove all entries in one loop through all
entries.

From a retest, the new remove_marked_cache_entries() from the patch
below, ended up with the following output line from oprofile:

46        0.0105  15        0.0041  git                      remove_marked_cache_entries

If we can trust the numbers from oprofile in this case, we saved
approximately ((7710 - 46) * 20000) / (2 * 1000 * 1000 * 1000) = 0.077
seconds CPU time with this fix for this particular test.  And notice
that now the CPU did only 46 / 15 = 3.1 cycles/instruction.
Signed-off-by: NKjetil Barvik <barvik@broadpark.no>
Acked-by: NLinus Torvalds <torvalds@linux-foundation.org>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

After you resolve a conflicted merge to remove the path, "git add -u"
failed to record the removal.  Instead it errored out by saying that the
removed path is not found in the work tree, but that is what the user
already knows, and the wanted to record the removal as the resolution,
so the error does not make sense.
Signed-off-by: NJunio C Hamano <gitster@pobox.com>

This simplifies the code, and also makes ce_compare_link now able to
handle filesystems with odd 'st_size' return values for symlinks.
Signed-off-by: NLinus Torvalds <torvalds@linux-foundation.org>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>