First of all, Ramsay, it would be great if you could test the below
patch and see if it works on Cygwin. I assume since Cygwin shares the
underlying filesystem, it will share the same "no trusting inode"
issue with native builds (or it calculates inodes anyway using some
other source?).

Back to the APFS problem...

On Mon, Nov 19, 2018 at 07:24:26PM +0100, Duy Nguyen wrote:
> Could you send me the "index" file in  t/trash\
> directory.t5601-clone/icasefs/bogus/.git/index ? Also the output of
> "stat /path/to/icase/bogus/x"
> 
> My only explanation is somehow the inode value we save is not the same
> one on disk, which is weird and could even cause other problems. I'd
> like to know why this happens before trying to fix anything.

Thanks Carlo for the file and "stat" output. The problem is APFS has
64-bit inode (according to the Internet) while we store inodes as
32-bit, so it's truncated. Which means this comparison

    sd_ino == st_ino

is never true because sd_ino is truncated (0x2121063) while st_ino is
not (0x202121063).

Carlo, it would be great if you could test this patch also with
APFS. It should fix problem. We will have to deal with the same
truncated inode elsewhere to make sure we index refresh performance
does not degrade on APFS. But that's a separate problem. Thank you for
bringing this up.

-- 8< --
diff --git a/entry.c b/entry.c
index 5d136c5d55..809d3e2ba7 100644
--- a/entry.c
+++ b/entry.c
@@ -404,13 +404,13 @@ static void mark_colliding_entries(const struct checkout 
*state,
 {
        int i, trust_ino = check_stat;
 
-#if defined(GIT_WINDOWS_NATIVE)
+#if defined(GIT_WINDOWS_NATIVE) || defined(__CYGWIN__)
        trust_ino = 0;
 #endif
 
        ce->ce_flags |= CE_MATCHED;
 
-       for (i = 0; i < state->istate->cache_nr; i++) {
+       for (i = 0; i < trust_ino && state->istate->cache_nr; i++) {
                struct cache_entry *dup = state->istate->cache[i];
 
                if (dup == ce)
@@ -419,10 +419,24 @@ static void mark_colliding_entries(const struct checkout 
*state,
                if (dup->ce_flags & (CE_MATCHED | CE_VALID | CE_SKIP_WORKTREE))
                        continue;
 
-               if ((trust_ino && dup->ce_stat_data.sd_ino == st->st_ino) ||
-                   (!trust_ino && !fspathcmp(ce->name, dup->name))) {
+               if (dup->ce_stat_data.sd_ino == (unsigned int)st->st_ino) {
                        dup->ce_flags |= CE_MATCHED;
+                       return;
+               }
+       }
+
+       for (i = 0; i < state->istate->cache_nr; i++) {
+               struct cache_entry *dup = state->istate->cache[i];
+
+               if (dup == ce)
                        break;
+
+               if (dup->ce_flags & (CE_MATCHED | CE_VALID | CE_SKIP_WORKTREE))
+                       continue;
+
+               if (!fspathcmp(ce->name, dup->name)) {
+                       dup->ce_flags |= CE_MATCHED;
+                       return;
                }
        }
 }
diff --git a/t/t5601-clone.sh b/t/t5601-clone.sh
index f1a49e94f5..c28d51bd59 100755
--- a/t/t5601-clone.sh
+++ b/t/t5601-clone.sh
@@ -628,7 +628,7 @@ test_expect_success 'clone on case-insensitive fs' '
        )
 '
 
-test_expect_success !MINGW,!CYGWIN,CASE_INSENSITIVE_FS 'colliding file 
detection' '
+test_expect_success !MINGW,CASE_INSENSITIVE_FS 'colliding file detection' '
        grep X icasefs/warning &&
        grep x icasefs/warning &&
        test_i18ngrep "the following paths have collided" icasefs/warning
-- 8< --

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