I'm confused how to revert changes in working tree:

$ git fetch
$ git merge "sync with origin" HEAD origin
....conflict....

$ git branch
* master
  origin

$ git status
# .....: needs update
# .....: needs update
(In fact I never modified anything in this tree, and "git diff"
showed many difference indeed, very strange).

I tried "git update-index --refresh", "git reset --hard",
"git reset --hard master", "git checkout master", 
"git checkout -f master", but "git status" still said same
as above.

At last, I deleted all files that were reported to be updated
with "rm -rf", ran "git checkout master" and "git status", then
git reported:
#       deleted:    ....
#       deleted:    ....

I use git-1.4.3.4.gbd45 under cygwin.
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That's windows and cygwin for you. They work together
and may someday even figure how to commit the changes.

They problem is the exec-bit which windows does not
have and cygwin failed to correctly workaround the
limitation.

Do a "git repo-config core.filemode false" to almost

After git update-index --refresh you shouldn't have had

Now do a git reset --hard and you should be set,
unless you're unlucky enough to work on FAT,
where probably nothing will save you.

And avoid using any "special" characters (8bit, utf/unicode)
in filenames, while you're on windows: you'll never be able
to share the repository (unless others agree to use your
rules for language and filesystem encoding).
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It's said somewhere "git pull" has strange behaviour and fetch+pull

sorry, I made a mistake, that should come from "git merge",
here is the message from "git status":
# Changed but not updated:
#   (use git-update-index to mark for commit)
#
#       modified:   include/linux/netfilter/xt_CONNMARK.h
#       modified:   include/linux/netfilter/xt_DSCP.h
#       modified:   include/linux/netfilter/xt_MARK.h
#       modified:   include/linux/netfilter_ipv4/ipt_CONNMARK.h
#       modified:   include/linux/netfilter_ipv4/ipt_DSCP.h
#       modified:   include/linux/netfilter_ipv4/ipt_ECN.h
#       modified:   include/linux/netfilter_ipv4/ipt_MARK.h
#       modified:   include/linux/netfilter_ipv4/ipt_TCPMSS.h
#       modified:   include/linux/netfilter_ipv4/ipt_TOS.h
#       modified:   include/linux/netfilter_ipv4/ipt_TTL.h
#       modified:   include/linux/netfilter_ipv6/ip6t_HL.h
#       modified:   include/linux/netfilter_ipv6/ip6t_MARK.h
#       modified:   net/ipv4/netfilter/ipt_ECN.c
#       modified:   net/ipv4/netfilter/ipt_TOS.c
#       modified:   net/ipv4/netfilter/ipt_TTL.c
#       modified:   net/ipv6/netfilter/ip6t_HL.c
#       modified:   net/netfilter/xt_CONNMARK.c
#       modified:   net/netfilter/xt_DSCP.c
#       modified:   net/netfilter/xt_MARK.c
#


It has been set. I guess the cause is a interrupted merge

After run "git reset --hard", all deleted files come back, but I reach
the old state:
$ git status
# Changed but not updated:
#   (use git-update-index to mark for commit)
#
#       modified:   include/linux/netfilter/xt_CONNMARK.h
#       modified:   include/linux/netfilter/xt_DSCP.h
...
#       modified:   net/netfilter/xt_MARK.c
#
In fact, I'm operating the linux-2.6 tree, so no special characters.


HEAD: commit 088406bcf66d6c7fd8a5c04c00aa410ae9077403
master: commit 088406bcf66d6c7fd8a5c04c00aa410ae9077403
origin: commit ff51a98799931256b555446b2f5675db08de6229
"git diff --cached" shows nothing;
"git diff" shows many diffs:

diff --git...
[ message continues ]

so, you just have an unresolved merge.
It was discussed on this mailing list very recently
(and actually is being discussed), so just look at

yes, though what I can't understand is why don't you have
unmerged entries... Maybe it comes from playing with

When? Immediately after git reset --hard? Then you very
likely have no permission to write (or lost it somehow) into
the working directory, otherwise I don't see could this be


and this is not. You do have changes, which could not be reset.
I fail to see why. Are you sure you haven't accidentally repeated
the merge after doing git reset --hard? And what was _exactly_
git merge told you, when it failed?
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Yes, immediately after git reset --hard. I'm sure I have write
permission because all deleted files come back and no "permission
denied" like message appears.

I didn't run "git merge" after "git reset --hard" indeed. To get the message
from "git merge", now I run it like this:

$ git merge "sync from origin" HEAD origin
Updating 088406b..ff51a98
include/linux/netfilter/xt_CONNMARK.h: needs update
include/linux/netfilter/xt_DSCP.h: needs update
include/linux/netfilter/xt_MARK.h: needs update
include/linux/netfilter_ipv4/ipt_CONNMARK.h: needs update
include/linux/netfilter_ipv4/ipt_DSCP.h: needs update
include/linux/netfilter_ipv4/ipt_ECN.h: needs update
include/linux/netfilter_ipv4/ipt_MARK.h: needs update
include/linux/netfilter_ipv4/ipt_TCPMSS.h: needs update
include/linux/netfilter_ipv4/ipt_TOS.h: needs update
include/linux/netfilter_ipv4/ipt_TTL.h: needs update
include/linux/netfilter_ipv6/ip6t_HL.h: needs update
include/linux/netfilter_ipv6/ip6t_MARK.h: needs update
net/ipv4/netfilter/ipt_ECN.c: needs update
net/ipv4/netfilter/ipt_TOS.c: needs update
net/ipv4/netfilter/ipt_TTL.c: needs update
net/ipv6/netfilter/ip6t_HL.c: needs update
net/netfilter/xt_CONNMARK.c: needs update
net/netfilter/xt_DSCP.c: needs update
net/netfilter/xt_MARK.c: needs update
fatal: Entry 'net/ipv4/netfilter/ipt_ECN.c' not uptodate. Cannot merge.

I really have never modified these files manually.
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You are just *very unlucky*.  :-)

The Linux kernel has case sensitive file names.  In other words there
are two files in the kernel:

  net/netfilter/xt_MARK.c
  net/netfilter/xt_mark.c

and they have different content!  On NTFS or FAT, where filenames
are not case sensitive, these become the same file.  So Git now
starts to think that the file was modified, because one of those
files overwrote the other when they were checked out.

Moral of the story: You cannot work with the linux.git repository
on a case insensitive filesystem, like NTFS, FAT (Windows), or HFS+
(Mac OS X).

-- 
Shawn.
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Yes, you are very right.

$ git ls-files |tr A-Z a-z | sort | uniq -c |grep -v "1 "
      2 include/linux/netfilter/xt_connmark.h
      2 include/linux/netfilter/xt_dscp.h
      2 include/linux/netfilter/xt_mark.h
      2 include/linux/netfilter_ipv4/ipt_connmark.h
      2 include/linux/netfilter_ipv4/ipt_dscp.h
      2 include/linux/netfilter_ipv4/ipt_ecn.h
      2 include/linux/netfilter_ipv4/ipt_mark.h
      2 include/linux/netfilter_ipv4/ipt_tcpmss.h
      2 include/linux/netfilter_ipv4/ipt_tos.h
      2 include/linux/netfilter_ipv4/ipt_ttl.h
      2 include/linux/netfilter_ipv6/ip6t_hl.h
      2 include/linux/netfilter_ipv6/ip6t_mark.h
      2 net/ipv4/netfilter/ipt_ecn.c
      2 net/ipv4/netfilter/ipt_tos.c
      2 net/ipv4/netfilter/ipt_ttl.c
      2 net/ipv6/netfilter/ip6t_hl.c
      2 net/netfilter/xt_connmark.c
      2 net/netfilter/xt_dscp.c
      2 net/netfilter/xt_mark.c

poor Windows... :-(
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Liu Yubao writes:
 > Yes, you are very right.
 > 
 > $ git ls-files |tr A-Z a-z | sort | uniq -c |grep -v "1 "
 >       2 include/linux/netfilter/xt_connmark.h
 >       2 include/linux/netfilter/xt_dscp.h
 >       2 include/linux/netfilter/xt_mark.h
 >       2 include/linux/netfilter_ipv4/ipt_connmark.h
 >       2 include/linux/netfilter_ipv4/ipt_dscp.h
 >       2 include/linux/netfilter_ipv4/ipt_ecn.h
 >       2 include/linux/netfilter_ipv4/ipt_mark.h
 >       2 include/linux/netfilter_ipv4/ipt_tcpmss.h
 >       2 include/linux/netfilter_ipv4/ipt_tos.h
 >       2 include/linux/netfilter_ipv4/ipt_ttl.h
 >       2 include/linux/netfilter_ipv6/ip6t_hl.h
 >       2 include/linux/netfilter_ipv6/ip6t_mark.h
 >       2 net/ipv4/netfilter/ipt_ecn.c
 >       2 net/ipv4/netfilter/ipt_tos.c
 >       2 net/ipv4/netfilter/ipt_ttl.c
 >       2 net/ipv6/netfilter/ip6t_hl.c
 >       2 net/netfilter/xt_connmark.c
 >       2 net/netfilter/xt_dscp.c
 >       2 net/netfilter/xt_mark.c
 > 
 > poor Windows... :-(

Incidentally I have this in my tree for a while, but it is not good
enough for general use, because you really need the original (not
lowercased) file names to resolve the problem. But my shell scripting
magic is not up to that task.

diff --git a/templates/hooks--pre-commit b/templates/hooks--pre-commit
index 723a9ef..0ceb01b 100644
--- a/templates/hooks--pre-commit
+++ b/templates/hooks--pre-commit
@@ -7,6 +7,17 @@
 #
 # To enable this hook, make this file executable.

+# Detect case challenges
+
+case_challenge=`git ls-files | tr A-Z a-z | sort | uniq -d`
+if [ -n "$case_challenge" ]
+then
+       echo >&2 "index contains file names differing only in case."
+       echo >&2 "lowercase names follow:"
+       echo >&2 "$case_challenge"
+       exit 1
+fi
+
 # This is slightly modified from Andrew Morton's Perfect Patch.
 # Lines you introduce should not have trailing whitespace.
 ...
[ message continues ]

Maybe you have the files open in some editor?
Otherwise something is broken. Could you try current git

don't think It'd be as simple as step-by-step in debugger.
Try to instrument builtin-read-tree.c or unpack-trees.c and

just for fun, what does following print:

  git read-tree --reset -u HEAD && git update-index --refresh

?
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