We parse each patchfile and find to what path it applies to and then
use that name to consult the attribute system to find what
whitespace rules to be applied, and also which target file (either
in the working tree or in the index) to replay the changes the patch
represents.

A non-Git patch is taken as relative to the current working
directory, and the prefix_patches() helper function introduced in
56185f49 (git-apply: require -p<n> when working in a subdirectory.,
2007-02-19) is used to prepend the prefix to these names found in
the patch input.

However, this prepending of the prefix to the pathnames is done
after the patch is fully parsed and affects only what target files
are patched.  Because the attributes are checked against the names
found in the patch during the parsing, not against the final path,
whitespace checks that are done during parsing end up using
attributes for a wrong path.

Because a Git-generated patch records the full path to the target
with -p$n prefix (e.g. a/ and b/) and we apply it relative to the
top of the working tree, prefix_patches() is a no-op and this
problem does not manifest for them.

Signed-off-by: Junio C Hamano <gits...@pobox.com>
---
 builtin/apply.c         | 41 +++++++++++++++++++----------------------
 t/t4119-apply-config.sh | 17 +++++++++++++++++
 2 files changed, 36 insertions(+), 22 deletions(-)

diff --git a/builtin/apply.c b/builtin/apply.c
index 6013e19..4270cde 100644
--- a/builtin/apply.c
+++ b/builtin/apply.c
@@ -1920,6 +1920,23 @@ static int parse_binary(char *buffer, unsigned long 
size, struct patch *patch)
        return used;
 }
 
+static void prefix_one(char **name)
+{
+       char *old_name = *name;
+       if (!old_name)
+               return;
+       *name = xstrdup(prefix_filename(prefix, prefix_length, *name));
+       free(old_name);
+}
+
+static void prefix_patch(struct patch *p)
+{
+       if (!prefix || p->is_toplevel_relative)
+               return;
+       prefix_one(&p->new_name);
+       prefix_one(&p->old_name);
+}
+
 /*
  * Read the patch text in "buffer" that extends for "size" bytes; stop
  * reading after seeing a single patch (i.e. changes to a single file).
@@ -1935,6 +1952,8 @@ static int parse_chunk(char *buffer, unsigned long size, 
struct patch *patch)
        if (offset < 0)
                return offset;
 
+       prefix_patch(patch);
+
        patch->ws_rule = whitespace_rule(patch->new_name
                                         ? patch->new_name
                                         : patch->old_name);
@@ -4164,26 +4183,6 @@ static int use_patch(struct patch *p)
        return !has_include;
 }
 
-
-static void prefix_one(char **name)
-{
-       char *old_name = *name;
-       if (!old_name)
-               return;
-       *name = xstrdup(prefix_filename(prefix, prefix_length, *name));
-       free(old_name);
-}
-
-static void prefix_patches(struct patch *p)
-{
-       if (!prefix || p->is_toplevel_relative)
-               return;
-       for ( ; p; p = p->next) {
-               prefix_one(&p->new_name);
-               prefix_one(&p->old_name);
-       }
-}
-
 #define INACCURATE_EOF (1<<0)
 #define RECOUNT                (1<<1)
 
@@ -4209,8 +4208,6 @@ static int apply_patch(int fd, const char *filename, int 
options)
                        break;
                if (apply_in_reverse)
                        reverse_patches(patch);
-               if (prefix)
-                       prefix_patches(patch);
                if (use_patch(patch)) {
                        patch_stats(patch);
                        *listp = patch;
diff --git a/t/t4119-apply-config.sh b/t/t4119-apply-config.sh
index 3d0384d..be325fa 100755
--- a/t/t4119-apply-config.sh
+++ b/t/t4119-apply-config.sh
@@ -159,4 +159,21 @@ test_expect_success 'same but with traditional patch input 
of depth 2' '
        check_result sub/file1
 '
 
+test_expect_success 'in subdir with traditional patch input' '
+       cd "$D" &&
+       git config apply.whitespace strip &&
+       cat >.gitattributes <<-EOF &&
+       /* whitespace=blank-at-eol
+       sub/* whitespace=-blank-at-eol
+       EOF
+       rm -f sub/file1 &&
+       cp saved sub/file1 &&
+       git update-index --refresh &&
+
+       cd sub &&
+       git apply ../gpatch.file &&
+       echo "B " >expect &&
+       test_cmp expect file1
+'
+
 test_done
-- 
2.1.0-rc1-209-g4e1b551

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