index-pack --strict looks up and follows parent commits. If shallow
information is not ready by the time index-pack is run, index-pack may
be lead to non-existent objects. Make fetch-pack save shallow file to
disk before invoking index-pack.

git learns new global option --shallow-file to pass on the alternate
shallow file path. Undocumented (and not even support --shallow-file=
syntax) because it's unlikely to be used again elsewhere.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclo...@gmail.com>
---
 commit.h              |  2 ++
 fetch-pack.c          | 69 +++++++++++++++++++++++++--------------------------
 git.c                 |  5 ++++
 shallow.c             | 45 +++++++++++++++++++++++++++++++--
 t/t5500-fetch-pack.sh |  7 ++++++
 5 files changed, 91 insertions(+), 37 deletions(-)

diff --git a/commit.h b/commit.h
index 67bd509..6e9c7cd 100644
--- a/commit.h
+++ b/commit.h
@@ -176,6 +176,8 @@ extern int for_each_commit_graft(each_commit_graft_fn, void 
*);
 extern int is_repository_shallow(void);
 extern struct commit_list *get_shallow_commits(struct object_array *heads,
                int depth, int shallow_flag, int not_shallow_flag);
+extern void check_shallow_file_for_update(void);
+extern void set_alternate_shallow_file(const char *path);
 
 int is_descendant_of(struct commit *, struct commit_list *);
 int in_merge_bases(struct commit *, struct commit *);
diff --git a/fetch-pack.c b/fetch-pack.c
index f156dd4..1ca4f6b 100644
--- a/fetch-pack.c
+++ b/fetch-pack.c
@@ -20,6 +20,8 @@ static int no_done;
 static int fetch_fsck_objects = -1;
 static int transfer_fsck_objects = -1;
 static int agent_supported;
+static struct lock_file shallow_lock;
+static const char *alternate_shallow_file;
 
 #define COMPLETE       (1U << 0)
 #define COMMON         (1U << 1)
@@ -683,7 +685,7 @@ static int get_pack(struct fetch_pack_args *args,
                    int xd[2], char **pack_lockfile)
 {
        struct async demux;
-       const char *argv[20];
+       const char *argv[22];
        char keep_arg[256];
        char hdr_arg[256];
        const char **av;
@@ -724,6 +726,11 @@ static int get_pack(struct fetch_pack_args *args,
                        do_keep = 1;
        }
 
+       if (alternate_shallow_file) {
+               *av++ = "--shallow-file";
+               *av++ = alternate_shallow_file;
+       }
+
        if (do_keep) {
                if (pack_lockfile)
                        cmd.out = -1;
@@ -779,6 +786,23 @@ static int cmp_ref_by_name(const void *a_, const void *b_)
        return strcmp(a->name, b->name);
 }
 
+static void setup_alternate_shallow(void)
+{
+       struct strbuf sb = STRBUF_INIT;
+       int fd;
+
+       check_shallow_file_for_update();
+       fd = hold_lock_file_for_update(&shallow_lock, git_path("shallow"),
+                                      LOCK_DIE_ON_ERROR);
+       if (write_shallow_commits(&sb, 0)) {
+               if (write_in_full(fd, sb.buf, sb.len) != sb.len)
+                       die_errno("failed to write to %s", 
shallow_lock.filename);
+               alternate_shallow_file = shallow_lock.filename;
+       } else
+               alternate_shallow_file = "";
+       strbuf_release(&sb);
+}
+
 static struct ref *do_fetch_pack(struct fetch_pack_args *args,
                                 int fd[2],
                                 const struct ref *orig_ref,
@@ -858,6 +882,8 @@ static struct ref *do_fetch_pack(struct fetch_pack_args 
*args,
 
        if (args->stateless_rpc)
                packet_flush(fd[1]);
+       if (args->depth > 0)
+               setup_alternate_shallow();
        if (get_pack(args, fd, pack_lockfile))
                die("git fetch-pack: fetch failed.");
 
@@ -936,15 +962,9 @@ struct ref *fetch_pack(struct fetch_pack_args *args,
                       struct ref **sought, int nr_sought,
                       char **pack_lockfile)
 {
-       struct stat st;
        struct ref *ref_cpy;
 
        fetch_pack_setup();
-       if (args->depth > 0) {
-               if (stat(git_path("shallow"), &st))
-                       st.st_mtime = 0;
-       }
-
        if (nr_sought)
                nr_sought = remove_duplicates_in_refs(sought, nr_sought);
 
@@ -955,34 +975,13 @@ struct ref *fetch_pack(struct fetch_pack_args *args,
        ref_cpy = do_fetch_pack(args, fd, ref, sought, nr_sought, 
pack_lockfile);
 
        if (args->depth > 0) {
-               static struct lock_file lock;
-               struct cache_time mtime;
-               struct strbuf sb = STRBUF_INIT;
-               char *shallow = git_path("shallow");
-               int fd;
-
-               mtime.sec = st.st_mtime;
-               mtime.nsec = ST_MTIME_NSEC(st);
-               if (stat(shallow, &st)) {
-                       if (mtime.sec)
-                               die("shallow file was removed during fetch");
-               } else if (st.st_mtime != mtime.sec
-#ifdef USE_NSEC
-                               || ST_MTIME_NSEC(st) != mtime.nsec
-#endif
-                         )
-                       die("shallow file was changed during fetch");
-
-               fd = hold_lock_file_for_update(&lock, shallow,
-                                              LOCK_DIE_ON_ERROR);
-               if (!write_shallow_commits(&sb, 0)
-                || write_in_full(fd, sb.buf, sb.len) != sb.len) {
-                       unlink_or_warn(shallow);
-                       rollback_lock_file(&lock);
-               } else {
-                       commit_lock_file(&lock);
-               }
-               strbuf_release(&sb);
+               struct stat st;
+               if (!fstat(shallow_lock.fd, &st) &&
+                   st.st_size == 0) {
+                       unlink_or_warn(git_path("shallow"));
+                       rollback_lock_file(&shallow_lock);
+               } else
+                       commit_lock_file(&shallow_lock);
        }
 
        reprepare_packed_git();
diff --git a/git.c b/git.c
index 1ada169..6450a38 100644
--- a/git.c
+++ b/git.c
@@ -4,6 +4,7 @@
 #include "help.h"
 #include "quote.h"
 #include "run-command.h"
+#include "commit.h"
 
 const char git_usage_string[] =
        "git [--version] [--help] [-c name=value]\n"
@@ -146,6 +147,10 @@ static int handle_options(const char ***argv, int *argc, 
int *envchanged)
                        setenv(GIT_LITERAL_PATHSPECS_ENVIRONMENT, "0", 1);
                        if (envchanged)
                                *envchanged = 1;
+               } else if (!strcmp(cmd, "--shallow-file")) {
+                       (*argv)++;
+                       (*argc)--;
+                       set_alternate_shallow_file((*argv)[0]);
                } else {
                        fprintf(stderr, "Unknown option: %s\n", cmd);
                        usage(git_usage_string);
diff --git a/shallow.c b/shallow.c
index 6be915f..bdae988 100644
--- a/shallow.c
+++ b/shallow.c
@@ -3,6 +3,16 @@
 #include "tag.h"
 
 static int is_shallow = -1;
+static struct stat shallow_stat;
+static char *alternate_shallow_file;
+
+void set_alternate_shallow_file(const char *path)
+{
+       if (is_shallow != -1)
+               die("BUG: is_repository_shallow must not be called before 
set_alternate_shallow_file");
+       free(alternate_shallow_file);
+       alternate_shallow_file = path ? xstrdup(path) : NULL;
+}
 
 int register_shallow(const unsigned char *sha1)
 {
@@ -21,12 +31,21 @@ int is_repository_shallow(void)
 {
        FILE *fp;
        char buf[1024];
+       const char *path = alternate_shallow_file;
 
        if (is_shallow >= 0)
                return is_shallow;
 
-       fp = fopen(git_path("shallow"), "r");
-       if (!fp) {
+       if (!path)
+               path = git_path("shallow");
+       /*
+        * fetch-pack set '--shallow-file ""' as an indicator that no
+        * shallow file should be used. We could just open it and it
+        * will likely fail. But let's do an explicit check instead.
+        */
+       if (!*path ||
+           stat(path, &shallow_stat) ||
+           (fp = fopen(path, "r")) == NULL) {
                is_shallow = 0;
                return is_shallow;
        }
@@ -108,3 +127,25 @@ struct commit_list *get_shallow_commits(struct 
object_array *heads, int depth,
 
        return result;
 }
+
+void check_shallow_file_for_update(void)
+{
+       struct stat st;
+
+       if (getenv("GIT_SHALLOW_FILE"))
+               die("GIT_SHALLOW_FILE should not be manually set");
+
+       if (!is_shallow)
+               return;
+       else if (is_shallow == -1)
+               die("BUG: shallow must be initialized by now");
+
+       if (stat(git_path("shallow"), &st))
+               die("shallow file was removed during fetch");
+       else if (st.st_mtime != shallow_stat.st_mtime
+#ifdef USE_NSEC
+                || ST_MTIME_NSEC(st) != ST_MTIME_NSEC(shallow_stat)
+#endif
+                  )
+               die("shallow file was changed during fetch");
+}
diff --git a/t/t5500-fetch-pack.sh b/t/t5500-fetch-pack.sh
index d574085..557b073 100755
--- a/t/t5500-fetch-pack.sh
+++ b/t/t5500-fetch-pack.sh
@@ -135,6 +135,13 @@ test_expect_success 'clone shallow depth 1' '
        test "`git --git-dir=shallow0/.git rev-list --count HEAD`" = 1
 '
 
+test_expect_success 'clone shallow depth 1 with fsck' '
+       git config --global fetch.fsckobjects true &&
+       git clone --no-single-branch --depth 1 "file://$(pwd)/." shallow0fsck &&
+       test "`git --git-dir=shallow0fsck/.git rev-list --count HEAD`" = 1 &&
+       git config --global --unset fetch.fsckobjects
+'
+
 test_expect_success 'clone shallow' '
        git clone --no-single-branch --depth 2 "file://$(pwd)/." shallow
 '
-- 
1.8.2.83.gc99314b

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