[RFC]Make stash a builtin

[rimrul]

This is mainly about e740d9e, the other commits are regular upstream commits.

stash--helper: implement "git stash--helper"

This patch implements a new "git stash--helper" builtin plumbing
command that will be used to migrate "git-stash.sh" to C.

We start by implementing only the "--non-patch" option that will
handle the core part of the non-patch stashing.

The other commits are in the pull request, because I based this on upstreams master. I want to introduce the stash--helper in another commit with a commit message simillar to 23b5f18 that contains this patch:

diff --git a/git-stash.sh b/git-stash.sh
index c7c65e2..c0f8b12 100755
--- a/git-stash.sh
+++ b/git-stash.sh
@@ -112,15 +112,9 @@ create_stash () {
    then

        # state of the working tree
-       w_tree=$( (
-           git read-tree --index-output="$TMPindex" -m $i_tree &&
-           GIT_INDEX_FILE="$TMPindex" &&
-           export GIT_INDEX_FILE &&
-           git diff --name-only -z HEAD -- >"$TMP-stagenames" &&
-           git update-index -z --add --remove --stdin <"$TMP-stagenames" &&
-           git write-tree &&
-           rm -f "$TMPindex"
-       ) ) ||
+       w_tree=$(
+       git stash--helper --non-patch $TMPindex $TMP-stagenames $i_tree
+       ) ||
            die "$(gettext "Cannot save the current worktree state")"

    else

[buildhive]

Git for Windows » git #23 FAILURE
Looks like there's a problem with this pull request
(what's this?)

[rimrul]

can confirm @buildhive. 48 breakages with t3903
EDIT: buildhive's complaint is about mergeconflicts

[dscho]

@rimrul it appears your branch is not forked off from Git for Windows' master, but probably from upstream's? We do not follow upstream that closely (yet), but only with released versions.

[rimrul]

48 breakages with t3903

Apparently t3903 runs into a SEGFAULT... Oh, the joys of C.

[dscho]

@rimrul why not rebase to Git for Windows' master?

[dscho]

@rimrul I promise to look at this PR again when it is rebased to master (into which it purports to want to be merged).

[rimrul]

@rimrul why not rebase to Git for Windows' master?

Mainly because I didn't think about the option to cherry pick this onto upstreams master.

@rimrul I promise to look at this PR again when it is rebased to master

Done. Sorry that it took me so long.

Apparently t3903 runs into a SEGFAULT

To be more precise, I get this output:

vagrant@vagrant-ubuntu-trusty-64:/vagrant/t$ echo 1 > file && git add file && echo unrelated >other-file && git add other-file && git commit -m initial && echo 2 > file && git add file && echo 3 > file && git stash                          17:55:12.686601 git.c:348               trace: built-in: git 'add' 'file'
17:55:12.725409 git.c:348               trace: built-in: git 'add' 'other-file'
17:55:12.758359 git.c:348               trace: built-in: git 'commit' '-m' 'initial'
[make-stash-a-builtin 9879adf] initial
 2 files changed, 2 insertions(+)
 create mode 100644 t/file
 create mode 100644 t/other-file
17:55:15.812020 git.c:348               trace: built-in: git 'add' 'file'
17:55:15.844950 git.c:561               trace: exec: 'git-stash'
17:55:15.845231 run-command.c:343       trace: run_command: 'git-stash'
17:55:15.850104 git.c:348               trace: built-in: git 'rev-parse' '--git-dir'
17:55:15.855297 git.c:348               trace: built-in: git 'rev-parse' '--git-path' 'objects'
17:55:15.864640 git.c:348               trace: built-in: git 'rev-parse' '--show-toplevel'
17:55:15.869640 git.c:348               trace: built-in: git 'rev-parse' '--git-path' 'index'
17:55:15.877152 git.c:348               trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
17:55:15.881917 git.c:348               trace: built-in: git 'config' '--get-color' 'color.interactive.help' 'red bold'
17:55:15.887258 git.c:348               trace: built-in: git 'config' '--get-color' '' 'reset'
17:55:15.892447 git.c:348               trace: built-in: git 'update-index' '-q' '--refresh'
17:55:16.394713 git.c:348               trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
17:55:16.448668 git.c:348               trace: built-in: git 'reflog' 'exists' 'refs/stash'
17:55:16.453418 git.c:348               trace: built-in: git 'update-index' '-q' '--refresh'
17:55:16.785993 git.c:348               trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
17:55:16.830562 git.c:348               trace: built-in: git 'rev-parse' '--verify' 'HEAD'
17:55:16.838658 git.c:348               trace: built-in: git 'rev-list' '--oneline' '-n' '1' 'HEAD' '--'
17:55:16.866326 git.c:348               trace: built-in: git 'symbolic-ref' '-q' 'HEAD'
17:55:16.871338 git.c:348               trace: built-in: git 'write-tree'
17:55:16.965126 git.c:348               trace: built-in: git 'commit-tree' 'f5acef6b2be517c49e5528789cf820d9c16be9a2' '-p' '9879adf5bf6c626d3d526cf8b0d866def4758656'
17:55:16.995261 git.c:348               trace: built-in: git 'stash--helper' '--non-patch' '.git/index.stash.10757' '/vagrant/.git/.git-stash.10757-stagenames' 'f5acef6b2be517c49e5528789cf820d9c16be9a2'
Segmentation fault (core dumped)
Cannot save the current worktree state

I tried to insert a printf("stash helper\n\n"); in the first line builtin/stash--helper.c, but it doesn't print. If I run git stash--helper I get the expected result:

git stash--helper
18:00:18.847398 git.c:348               trace: built-in: git 'stash--helper'
stash helper

fatal: Usage: git stash--helper --non-patch <tmp_indexfile> <tmp_stagefile> <i_tree>

I'm slightly confused. Do I call this wrong in git-stash.sh?

[rimrul]

I tried to insert a printf("stash helper\n\n"); in the first line builtin/stash--helper.c, but it doesn't print. If I run git stash--helper I get the expected result:
I'm slightly confused. Do I call this wrong in git-stash.sh?

I found that issue. Printing debug messages to stdout and collecting stdout into a shell variable don't mix too well.

[dscho]

Good point! fprintf(stderr, ...); is your friend. Under certain circumstances, I found it necessary to fflush(stderr), too, usually when there is a segfault just after the print statement: in MinTTY, stderr is funneled through a pipe and is not really synchronous.

[rimrul]

So I'm getting closer, but there are these lines git-stash.sh#L119-L120 that won't work with the run-command API. Trying to run them with system() doesn't succeed either. I might work around this for the first line with the diff API, but I don't see a way to get this second line to work. Except for reopening stdin and directly calling main(). But I'm sure upstream wont accept that. Also this would probably result in the first non spam related permanent ban from the mailing list.

[rimrul]

Except for reopening stdin and directly calling main().

Reopening stdin and calling run_command() should work too, but the cleanup with dup2() would be non-standard at best.

[rimrul]

I might work around this for the first line with the diff API

No, this doesn't work either.

[rimrul]

So I'm getting closer, but there are these lines git-stash.sh#L119-L120 that won't work with the run-command API. Trying to run them with system() doesn't succeed either. I might work around this for the first line with the diff API, but I don't see a way to get this second line to work. Except for reopening stdin and directly calling main(). But I'm sure upstream wont accept that. Also this would probably result in the first non spam related permanent ban from the mailing list.

.

Except for reopening stdin and directly calling main().

Reopening stdin and calling run_command() should work too, but the cleanup with dup2() would be non-standard at best.

.

I might work around this for the first line with the diff API

No, this doesn't work either.

I could probably get this to work with capture_command() and building an argv for git update-index that doesn't involve stdin. This would also get rid of tmp_stagefile.

[rimrul]

I just f-ed up bigtime. I had it working. Still breaking 3 things in t3903, but working. But I did't commit it before running t3903, a test, that includes stashing all changes and removing the stash... I think you know the result.

[rimrul]

I just f-ed up bigtime. I had it working. Still breaking 3 things in t3903, but working. But I did't commit it before running t3903, a test, that includes stashing all changes and removing the stash... I think you know the result.

Update: I managed to restore git-stash.sh, builtin/stash--helper.c and stash.h to their state before the accident. I'm pushing this even though it won't compile because I'll still have to recreate stash.c.

We should keep a reference to 86a8da04b7 and 8a20aa83b2, because some of the discussion happened on line comments.

[dscho]

I'll still have to recreate stash.c.

If you ever staged it (including a stash), it should be found by git fsck --lost-found.

[rimrul]

I'll still have to recreate stash.c.
If you ever staged it (including a stash), it should be found by git fsck --lost-found.

Sadly neither git fsck --lost-found nor git fsck --no-reflog nor git fsck --unreachable yield a stash that contains this file. Most results are index on-commits, that can't be applied by git stash apply. I roughly know what I did, that made it work though.

[rimrul]

I'll still have to recreate stash.c.

I have recreated it, but I think I missed something. It still has 31 breakages in t3903... And I didn't even test the three other tests for stash.

[rimrul]

I have recreated it, but I think I missed something. It still has 31 breakages in t3903... And I didn't even test the three other tests for stash.

I got them down to two. t3904, t3905 and t3906 pass fine now.

[rimrul]

I have no clue how I break git stash apply and/or git status for test 52 and git log -g --format="%cd" -1 refs/stash for test 56.

[rimrul]

I've rebased this onto the current tip of master. I've found the point of failure for t3903.52, but I can't seem to reproduce it outside of t3903. Below is a traced run of t3903.

vagrant@vagrant-ubuntu-trusty-64:/vagrant/t$ GIT_TRACE=1 ./t3903-stash.sh --verbose-only=5[26]
ok 1 - stash some dirty working directory
ok 2 - parents of stash
ok 3 - applying bogus stash does nothing
ok 4 - apply does not need clean working directory
ok 5 - apply does not clobber working directory changes
ok 6 - apply stashed changes
ok 7 - apply stashed changes (including index)
ok 8 - unstashing in a subdirectory
ok 9 - stash drop complains of extra options
ok 10 - drop top stash
ok 11 - drop middle stash
ok 12 - stash pop
ok 13 - stash branch
ok 14 - apply -q is quiet
ok 15 - save -q is quiet
ok 16 - pop -q is quiet
ok 17 - pop -q --index works and is quiet
ok 18 - drop -q is quiet
ok 19 - stash -k
ok 20 - stash --no-keep-index
ok 21 - stash --invalid-option
ok 22 - stash an added file
ok 23 - stash rm then recreate
ok 24 - stash rm and ignore
ok 25 - stash rm and ignore (stage .gitignore)
ok 26 # skip stash file to symlink (missing SYMLINKS)
ok 27 # skip stash file to symlink (stage rm) (missing SYMLINKS)
ok 28 # skip stash file to symlink (full stage) (missing SYMLINKS)
ok 29 - stash symlink to file
ok 30 # skip this must have re-created the symlink (missing SYMLINKS)
ok 31 - unstash must re-create the file
ok 32 - stash symlink to file (stage rm)
ok 33 # skip this must have re-created the symlink (missing SYMLINKS)
ok 34 - unstash must re-create the file
ok 35 - stash symlink to file (full stage)
ok 36 # skip this must have re-created the symlink (missing SYMLINKS)
ok 37 - unstash must re-create the file
not ok 38 - stash directory to file # TODO known breakage
not ok 39 - stash file to directory # TODO known breakage
ok 40 - stash branch - no stashes on stack, stash-like argument
ok 41 - stash branch - stashes on stack, stash-like argument
ok 42 - stash show format defaults to --stat
ok 43 - stash show - stashes on stack, stash-like argument
ok 44 - stash show -p - stashes on stack, stash-like argument
ok 45 - stash show - no stashes on stack, stash-like argument
ok 46 - stash show -p - no stashes on stack, stash-like argument
ok 47 - stash drop - fail early if specified stash is not a stash reference
ok 48 - stash pop - fail early if specified stash is not a stash reference
ok 49 - ref with non-existent reflog
ok 50 - invalid ref of the form stash@{n}, n >= N
ok 51 - stash branch should not drop the stash if the branch exists

expecting success:
        git stash clear &&
        echo 1 >subdir/subfile1 &&
        echo 2 >subdir/subfile2 &&
        git add subdir/subfile1 &&
        git commit -m subdir &&
        (
                cd subdir &&
                echo x >subfile1 &&
                echo x >../file &&
                git status >../expect &&
                git stash &&
                sane_unset GIT_MERGE_VERBOSITY &&
                git stash apply
        ) |
        sed -e 1,2d >actual && # drop "Saved..." and "HEAD is now..."
        test_i18ncmp expect actual

trace: exec: 'git-stash' 'clear'
trace: run_command: 'git-stash' 'clear'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash'
trace: built-in: git 'update-ref' '-d' 'refs/stash' 'baeaed7e0e8746d0ca3c109ae52a0a49cc2043d6'
trace: built-in: git 'add' 'subdir/subfile1'
trace: built-in: git 'commit' '-m' 'subdir'
[master 307367e] subdir
 Author: A U Thor <author@example.com>
 1 file changed, 1 insertion(+)
 create mode 100644 subdir/subfile1
trace: built-in: git 'status'
trace: exec: 'git-stash'
trace: run_command: 'git-stash'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
trace: built-in: git 'diff-files' '--quiet' '--ignore-submodules'
trace: built-in: git 'reflog' 'exists' 'refs/stash'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
trace: built-in: git 'diff-files' '--quiet' '--ignore-submodules'
trace: built-in: git 'rev-parse' '--verify' 'HEAD'
trace: built-in: git 'rev-list' '--oneline' '-n' '1' 'HEAD' '--'
trace: built-in: git 'symbolic-ref' '-q' 'HEAD'
trace: built-in: git 'write-tree'
trace: built-in: git 'commit-tree' '13419d0b4f5b097f61dde4c911de99a154f8286f' '-p' '307367ef082bbeb26ff4d37194044be1a75ff404'
trace: built-in: git 'stash--helper' '--non-patch' '.git/index.stash.29650' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: run_command: 'read-tree' '--index-output=.git/index.stash.29650' '-m' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: exec: 'git' 'read-tree' '--index-output=.git/index.stash.29650' '-m' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: built-in: git 'read-tree' '--index-output=.git/index.stash.29650' '-m' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: run_command: 'diff' '--name-only' '-z' 'HEAD' '--'
trace: exec: 'git' 'diff' '--name-only' '-z' 'HEAD' '--'
trace: built-in: git 'diff' '--name-only' '-z' 'HEAD' '--'
trace: run_command: 'update-index' '--add' '--remove' 'file' '--'
trace: exec: 'git' 'update-index' '--add' '--remove' 'file' '--'
trace: built-in: git 'update-index' '--add' '--remove' 'file' '--'
trace: run_command: 'write-tree'
trace: exec: 'git' 'write-tree'
trace: built-in: git 'write-tree'
trace: built-in: git 'commit-tree' '952e273ccfa63fb1b47f7463e0deea054576c60e' '-p' '307367ef082bbeb26ff4d37194044be1a75ff404' '-p' '5a272eb2d4d8819f7aed183172ebd3e8999b74c2'
trace: built-in: git 'update-ref' '--create-reflog' '-m' 'WIP on master: 307367e subdir' 'refs/stash' '8f8b5351a83d9d96b32d2dbecccce4bc801f666a'
trace: built-in: git 'reset' '--hard'
trace: exec: 'git-stash' 'apply'
trace: run_command: 'git-stash' 'apply'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'rev-parse' '--no-flags' '--symbolic' '--sq'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash'
trace: built-in: git 'rev-parse' '--symbolic' '--verify' '--quiet' 'refs/stash@{0}'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash@{0}^2'
trace: built-in: git 'rev-parse' 'refs/stash@{0}' 'refs/stash@{0}^1' 'refs/stash@{0}:' 'refs/stash@{0}^1:' 'refs/stash@{0}^2:'
trace: built-in: git 'rev-parse' '--symbolic-full-name' 'refs/stash'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash@{0}^3'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'write-tree'
trace: built-in: git 'merge-recursive' '13419d0b4f5b097f61dde4c911de99a154f8286f' '--' '13419d0b4f5b097f61dde4c911de99a154f8286f' '952e273ccfa63fb1b47f7463e0deea054576c60e'
trace: built-in: git 'diff-index' '--cached' '--name-only' '--diff-filter=A' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: built-in: git 'read-tree' '--reset' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: built-in: git 'update-index' '--add' '--stdin'
trace: built-in: git 'status'
--- expect      2016-01-15 19:22:41.868722800 +0000
+++ actual      2016-01-15 19:22:42.548464700 +0000
@@ -4,7 +4,6 @@
   (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   ../file
-       modified:   subfile1

 Untracked files:
   (use "git add <file>..." to include in what will be committed)
not ok 52 - stash apply shows status same as git status (relative to current directory)
#
#               git stash clear &&
#               echo 1 >subdir/subfile1 &&
#               echo 2 >subdir/subfile2 &&
#               git add subdir/subfile1 &&
#               git commit -m subdir &&
#               (
#                       cd subdir &&
#                       echo x >subfile1 &&
#                       echo x >../file &&
#                       git status >../expect &&
#                       git stash &&
#                       sane_unset GIT_MERGE_VERBOSITY &&
#                       git stash apply
#               ) |
#               sed -e 1,2d >actual && # drop "Saved..." and "HEAD is now..."
#               test_i18ncmp expect actual
#

ok 53 - stash where working directory contains "HEAD" file
ok 54 - store called with invalid commit
ok 55 - store updates stash ref and reflog

expecting success:
        git stash clear &&
        echo pig >file &&
        git stash &&
        stamp=$(git log -g --format="%cd" -1 refs/stash) &&
        test_tick &&
        echo cow >file &&
        git stash &&
        git stash apply "stash@{$stamp}" &&
        grep pig file

trace: exec: 'git-stash' 'clear'
trace: run_command: 'git-stash' 'clear'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash'
trace: exec: 'git-stash'
trace: run_command: 'git-stash'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
trace: built-in: git 'reflog' 'exists' 'refs/stash'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
trace: built-in: git 'rev-parse' '--verify' 'HEAD'
trace: built-in: git 'rev-list' '--oneline' '-n' '1' 'HEAD' '--'
trace: built-in: git 'symbolic-ref' '-q' 'HEAD'
trace: built-in: git 'write-tree'
trace: built-in: git 'commit-tree' 'd4f789cedf61d31fea45a20a8aeeb7f308215739' '-p' '307367ef082bbeb26ff4d37194044be1a75ff404'
trace: built-in: git 'stash--helper' '--non-patch' '.git/index.stash.29998' 'd4f789cedf61d31fea45a20a8aeeb7f308215739'
trace: run_command: 'read-tree' '--index-output=.git/index.stash.29998' '-m' 'd4f789cedf61d31fea45a20a8aeeb7f308215739'
trace: exec: 'git' 'read-tree' '--index-output=.git/index.stash.29998' '-m' 'd4f789cedf61d31fea45a20a8aeeb7f308215739'
trace: built-in: git 'read-tree' '--index-output=.git/index.stash.29998' '-m' 'd4f789cedf61d31fea45a20a8aeeb7f308215739'
trace: run_command: 'diff' '--name-only' '-z' 'HEAD' '--'
trace: exec: 'git' 'diff' '--name-only' '-z' 'HEAD' '--'
trace: built-in: git 'diff' '--name-only' '-z' 'HEAD' '--'
trace: run_command: 'update-index' '--add' '--remove' 'bazzy' '--'
trace: exec: 'git' 'update-index' '--add' '--remove' 'bazzy' '--'
trace: built-in: git 'update-index' '--add' '--remove' 'bazzy' '--'
trace: run_command: 'write-tree'
trace: exec: 'git' 'write-tree'
trace: built-in: git 'write-tree'
trace: built-in: git 'commit-tree' 'd4f789cedf61d31fea45a20a8aeeb7f308215739' '-p' '307367ef082bbeb26ff4d37194044be1a75ff404' '-p' 'e5f0c4dba2a136e602ccd9e0728b630ddb4bec6f'
trace: built-in: git 'update-ref' '--create-reflog' '-m' 'WIP on master: 307367e subdir' 'refs/stash' 'f7a049d0b388a9dc92adada4e0f83e8fc9497671'
Saved working directory and index state WIP on master: 307367e subdir
trace: built-in: git 'reset' '--hard'
HEAD is now at 307367e subdir
trace: built-in: git 'log' '-g' '--format=%cd' '-1' 'refs/stash'
trace: exec: 'git-stash'
trace: run_command: 'git-stash'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
trace: built-in: git 'diff-files' '--quiet' '--ignore-submodules'
trace: built-in: git 'reflog' 'exists' 'refs/stash'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'diff-index' '--quiet' '--cached' 'HEAD' '--ignore-submodules' '--'
trace: built-in: git 'diff-files' '--quiet' '--ignore-submodules'
trace: built-in: git 'rev-parse' '--verify' 'HEAD'
trace: built-in: git 'rev-list' '--oneline' '-n' '1' 'HEAD' '--'
trace: built-in: git 'symbolic-ref' '-q' 'HEAD'
trace: built-in: git 'write-tree'
trace: built-in: git 'commit-tree' '13419d0b4f5b097f61dde4c911de99a154f8286f' '-p' '307367ef082bbeb26ff4d37194044be1a75ff404'
trace: built-in: git 'stash--helper' '--non-patch' '.git/index.stash.30045' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: run_command: 'read-tree' '--index-output=.git/index.stash.30045' '-m' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: exec: 'git' 'read-tree' '--index-output=.git/index.stash.30045' '-m' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: built-in: git 'read-tree' '--index-output=.git/index.stash.30045' '-m' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: run_command: 'diff' '--name-only' '-z' 'HEAD' '--'
trace: exec: 'git' 'diff' '--name-only' '-z' 'HEAD' '--'
trace: built-in: git 'diff' '--name-only' '-z' 'HEAD' '--'
trace: run_command: 'update-index' '--add' '--remove' 'file' '--'
trace: exec: 'git' 'update-index' '--add' '--remove' 'file' '--'
trace: built-in: git 'update-index' '--add' '--remove' 'file' '--'
trace: run_command: 'write-tree'
trace: exec: 'git' 'write-tree'
trace: built-in: git 'write-tree'
trace: built-in: git 'commit-tree' 'f6a518ff4c4455fd91b5c1fa6459807a82f14226' '-p' '307367ef082bbeb26ff4d37194044be1a75ff404' '-p' '0ddc29bca4322a86999c2a4f30d6f71de9ad8ea9'
trace: built-in: git 'update-ref' '--create-reflog' '-m' 'WIP on master: 307367e subdir' 'refs/stash' '6c23291333c7bbacf40a3d32fc6ea643378e74d5'
Saved working directory and index state WIP on master: 307367e subdir
trace: built-in: git 'reset' '--hard'
HEAD is now at 307367e subdir
trace: exec: 'git-stash' 'apply' 'stash@{Thu Apr 7 15:17:13 2005 -0700}'
trace: run_command: 'git-stash' 'apply' 'stash@{Thu Apr 7 15:17:13 2005 -0700}'
trace: built-in: git 'rev-parse' '--git-dir'
trace: built-in: git 'rev-parse' '--git-path' 'objects'
trace: built-in: git 'rev-parse' '--is-inside-work-tree'
trace: built-in: git 'rev-parse' '--show-toplevel'
trace: built-in: git 'rev-parse' '--git-path' 'index'
trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
trace: built-in: git 'rev-parse' '--no-flags' '--symbolic' '--sq' 'stash@{Thu Apr 7 15:17:13 2005 -0700}'
trace: built-in: git 'rev-parse' '--symbolic' '--verify' '--quiet' 'stash@{Thu Apr 7 15:17:13 2005 -0700}'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'stash@{Thu Apr 7 15:17:13 2005 -0700}^2'
trace: built-in: git 'rev-parse' 'stash@{Thu Apr 7 15:17:13 2005 -0700}' 'stash@{Thu Apr 7 15:17:13 2005 -0700}^1' 'stash@{Thu Apr 7 15:17:13 2005 -0700}:' 'stash@{Thu Apr 7 15:17:13 2005 -0700}^1:' 'stash@{Thu Apr 7 15:17:13 2005 -0700}^2:'
trace: built-in: git 'rev-parse' '--symbolic-full-name' 'stash'
trace: built-in: git 'rev-parse' '--verify' '--quiet' 'stash@{Thu Apr 7 15:17:13 2005 -0700}^3'
trace: built-in: git 'update-index' '-q' '--refresh'
trace: built-in: git 'write-tree'
trace: built-in: git 'merge-recursive' '13419d0b4f5b097f61dde4c911de99a154f8286f' '--' '13419d0b4f5b097f61dde4c911de99a154f8286f' 'd4f789cedf61d31fea45a20a8aeeb7f308215739'
Merging Version stash was based on with Stashed changes
Merging:
virtual Version stash was based on
virtual Stashed changes
found 1 common ancestor:
virtual 13419d0b4f5b097f61dde4c911de99a154f8286f
trace: built-in: git 'diff-index' '--cached' '--name-only' '--diff-filter=A' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: built-in: git 'read-tree' '--reset' '13419d0b4f5b097f61dde4c911de99a154f8286f'
trace: built-in: git 'update-index' '--add' '--stdin'
trace: built-in: git 'status'
On branch master
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

        new file:   bazzy

Untracked files:
  (use "git add <file>..." to include in what will be committed)

        actual
        expect
        expect1
        expect2
        expected
        output
        output.out
        stashlist1
        stashlist2
        subdir/subfile2

not ok 56 - handle stash specification with spaces
#
#               git stash clear &&
#               echo pig >file &&
#               git stash &&
#               stamp=$(git log -g --format="%cd" -1 refs/stash) &&
#               test_tick &&
#               echo cow >file &&
#               git stash &&
#               git stash apply "stash@{$stamp}" &&
#               grep pig file
#

ok 57 - setup stash with index and worktree changes
ok 58 - stash list implies --first-parent -m
ok 59 - stash list --cc shows combined diff
# still have 2 known breakage(s)
# failed 2 among remaining 57 test(s)
1..59

I even tried to reproduce t3903.52 by calling ./t3903-stash.sh --run=-51 -d followed by GIT_TRACE=1 git stash clear && echo 1 >subdir/subfile1 && echo 2 >subdir/subfile2 && git add subdir/subfile1 && git commit -m subdir && ( cd subdir && echo x >subfile1 && echo x >../file && git status && git stash && git stash apply; ). I can't reproduce the issue that way either... Here is the output of my McGyver debug version of t3903.52:

vagrant@vagrant-ubuntu-trusty-64:/vagrant/t$ ./t3903-stash.sh --run=-51 -d
ok 1 - stash some dirty working directory
ok 2 - parents of stash
ok 3 - applying bogus stash does nothing
ok 4 - apply does not need clean working directory
ok 5 - apply does not clobber working directory changes
ok 6 - apply stashed changes
ok 7 - apply stashed changes (including index)
ok 8 - unstashing in a subdirectory
ok 9 - stash drop complains of extra options
ok 10 - drop top stash
ok 11 - drop middle stash
ok 12 - stash pop
ok 13 - stash branch
ok 14 - apply -q is quiet
ok 15 - save -q is quiet
ok 16 - pop -q is quiet
ok 17 - pop -q --index works and is quiet
ok 18 - drop -q is quiet
ok 19 - stash -k
ok 20 - stash --no-keep-index
ok 21 - stash --invalid-option
ok 22 - stash an added file
ok 23 - stash rm then recreate
ok 24 - stash rm and ignore
ok 25 - stash rm and ignore (stage .gitignore)
ok 26 # skip stash file to symlink (missing SYMLINKS)
ok 27 # skip stash file to symlink (stage rm) (missing SYMLINKS)
ok 28 # skip stash file to symlink (full stage) (missing SYMLINKS)
ok 29 - stash symlink to file
ok 30 # skip this must have re-created the symlink (missing SYMLINKS)
ok 31 - unstash must re-create the file
ok 32 - stash symlink to file (stage rm)
ok 33 # skip this must have re-created the symlink (missing SYMLINKS)
ok 34 - unstash must re-create the file
ok 35 - stash symlink to file (full stage)
ok 36 # skip this must have re-created the symlink (missing SYMLINKS)
ok 37 - unstash must re-create the file
not ok 38 - stash directory to file # TODO known breakage
not ok 39 - stash file to directory # TODO known breakage
ok 40 - stash branch - no stashes on stack, stash-like argument
ok 41 - stash branch - stashes on stack, stash-like argument
ok 42 - stash show format defaults to --stat
ok 43 - stash show - stashes on stack, stash-like argument
ok 44 - stash show -p - stashes on stack, stash-like argument
ok 45 - stash show - no stashes on stack, stash-like argument
ok 46 - stash show -p - no stashes on stack, stash-like argument
ok 47 - stash drop - fail early if specified stash is not a stash reference
ok 48 - stash pop - fail early if specified stash is not a stash reference
ok 49 - ref with non-existent reflog
ok 50 - invalid ref of the form stash@{n}, n >= N
ok 51 - stash branch should not drop the stash if the branch exists
ok 52 # skip stash apply shows status same as git status (relative to current directory) (--run)
ok 53 # skip stash where working directory contains "HEAD" file (--run)
ok 54 # skip store called with invalid commit (--run)
ok 55 # skip store updates stash ref and reflog (--run)
ok 56 # skip handle stash specification with spaces (--run)
ok 57 # skip setup stash with index and worktree changes (--run)
ok 58 # skip stash list implies --first-parent -m (--run)
ok 59 # skip stash list --cc shows combined diff (--run)
# still have 2 known breakage(s)
# passed all remaining 57 test(s)
1..59
vagrant@vagrant-ubuntu-trusty-64:/vagrant/t$ GIT_TRACE=1 git stash clear && echo 1 >subdir/subfile1 && echo 2 >subdir/subfile2 && git add subdir/subfile1 && git commit -m subdir && ( cd subdir && echo x >subfile1 && echo x >../file && git status && git stash && git stash apply; )
20:36:47.488772 git.c:562               trace: exec: 'git-stash' 'clear'
20:36:47.488846 run-command.c:343       trace: run_command: 'git-stash' 'clear'
20:36:47.494106 git.c:348               trace: built-in: git 'rev-parse' '--git-dir'
20:36:47.498399 git.c:348               trace: built-in: git 'rev-parse' '--git-path' 'objects'
20:36:47.506734 git.c:348               trace: built-in: git 'rev-parse' '--show-toplevel'
20:36:47.510918 git.c:348               trace: built-in: git 'rev-parse' '--git-path' 'index'
20:36:47.516292 git.c:348               trace: built-in: git 'config' '--get-colorbool' 'color.interactive'
20:36:47.519927 git.c:348               trace: built-in: git 'config' '--get-color' 'color.interactive.help' 'red bold'
20:36:47.523551 git.c:348               trace: built-in: git 'config' '--get-color' '' 'reset'
20:36:47.525743 git.c:348               trace: built-in: git 'rev-parse' '--verify' '--quiet' 'refs/stash'
20:36:47.534873 git.c:348               trace: built-in: git 'update-ref' '-d' 'refs/stash' '59aa6fcf4ca9a5ee6d1c7f9e3b0cccad7c152f7a'
[make-stash-a-builtin dac0ab3] subdir
 1 file changed, 1 insertion(+)
 create mode 100644 t/subdir/subfile1
On branch make-stash-a-builtin
Your branch is ahead of 'github/make-stash-a-builtin' by 1 commit.
  (use "git push" to publish your local commits)
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   subfile1

Untracked files:
  (use "git add <file>..." to include in what will be committed)

        ../../git-stash--helper
        ../expect
        ../file
        subfile2
        ../../trace3903.txt

no changes added to commit (use "git add" and/or "git commit -a")
Saved working directory and index state WIP on make-stash-a-builtin: dac0ab3 subdir
HEAD is now at dac0ab3 subdir
On branch make-stash-a-builtin
Your branch is ahead of 'github/make-stash-a-builtin' by 1 commit.
  (use "git push" to publish your local commits)
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   subfile1

Untracked files:
  (use "git add <file>..." to include in what will be committed)

        ../../git-stash--helper
        ../expect
        ../file
        subfile2
        ../../trace3903.txt

no changes added to commit (use "git add" and/or "git commit -a")

I have the slight feeling, that one of us is going insane and I'm not sure wether it's me or Git. I'd really appreciate, if someone could have a look at this. Am I missing something obvious? Is my test environment haunted?

[rimrul]

I found the issue. I didn't read the documentation for update-index -z properly. All tests ok, now.