I'll be sending a few patches that apply on top of applying these
two patches to show what I meant in my previous review comments.
The net change to apply.c, when you combine your 2/2 with these,
would become like the attached, which I think makes more sense.

Instead of queuing a squashed result, I thought it may help to send
them as incremental fixes with their own justification.

diff --git a/apply.c b/apply.c
index f2d599141d..c06f7014a2 100644
--- a/apply.c
+++ b/apply.c
@@ -220,6 +220,7 @@ struct patch {
        unsigned int recount:1;
        unsigned int conflicted_threeway:1;
        unsigned int direct_to_threeway:1;
+       unsigned int crlf_in_old:1;
        struct fragment *fragments;
        char *result;
        size_t resultsize;
@@ -1662,6 +1663,19 @@ static void check_whitespace(struct apply_state *state,
        record_ws_error(state, result, line + 1, len - 2, state->linenr);
 }
 
+/*
+ * Check if the patch has context lines with CRLF or
+ * the patch wants to remove lines with CRLF.
+ */
+static void check_old_for_crlf(struct patch *patch, const char *line, int len)
+{
+       if (len >= 2 && line[len-1] == '\n' && line[len-2] == '\r') {
+               patch->ws_rule |= WS_CR_AT_EOL;
+               patch->crlf_in_old = 1;
+       }
+}
+
+
 /*
  * Parse a unified diff. Note that this really needs to parse each
  * fragment separately, since the only way to know the difference
@@ -1712,11 +1726,14 @@ static int parse_fragment(struct apply_state *state,
                        if (!deleted && !added)
                                leading++;
                        trailing++;
+                       check_old_for_crlf(patch, line, len);
                        if (!state->apply_in_reverse &&
                            state->ws_error_action == correct_ws_error)
                                check_whitespace(state, line, len, 
patch->ws_rule);
                        break;
                case '-':
+                       if (!state->apply_in_reverse)
+                               check_old_for_crlf(patch, line, len);
                        if (state->apply_in_reverse &&
                            state->ws_error_action != nowarn_ws_error)
                                check_whitespace(state, line, len, 
patch->ws_rule);
@@ -1725,6 +1742,8 @@ static int parse_fragment(struct apply_state *state,
                        trailing = 0;
                        break;
                case '+':
+                       if (state->apply_in_reverse)
+                               check_old_for_crlf(patch, line, len);
                        if (!state->apply_in_reverse &&
                            state->ws_error_action != nowarn_ws_error)
                                check_whitespace(state, line, len, 
patch->ws_rule);
@@ -2268,8 +2287,12 @@ static void show_stats(struct apply_state *state, struct 
patch *patch)
                add, pluses, del, minuses);
 }
 
-static int read_old_data(struct stat *st, const char *path, struct strbuf *buf)
+static int read_old_data(struct stat *st, const char *path, struct strbuf *buf,
+                        struct patch *patch)
 {
+       enum safe_crlf safe_crlf = (patch->crlf_in_old
+                                   ? SAFE_CRLF_KEEP_CRLF : SAFE_CRLF_FALSE);
+
        switch (st->st_mode & S_IFMT) {
        case S_IFLNK:
                if (strbuf_readlink(buf, path, st->st_size) < 0)
@@ -2278,7 +2301,7 @@ static int read_old_data(struct stat *st, const char 
*path, struct strbuf *buf)
        case S_IFREG:
                if (strbuf_read_file(buf, path, st->st_size) != st->st_size)
                        return error(_("unable to open or read %s"), path);
-               convert_to_git(&the_index, path, buf->buf, buf->len, buf, 0);
+               convert_to_git(&the_index, path, buf->buf, buf->len, buf, 
safe_crlf);
                return 0;
        default:
                return -1;
@@ -3384,6 +3407,7 @@ static int load_patch_target(struct apply_state *state,
                             struct strbuf *buf,
                             const struct cache_entry *ce,
                             struct stat *st,
+                            struct patch *patch,
                             const char *name,
                             unsigned expected_mode)
 {
@@ -3399,7 +3423,7 @@ static int load_patch_target(struct apply_state *state,
                } else if (has_symlink_leading_path(name, strlen(name))) {
                        return error(_("reading from '%s' beyond a symbolic 
link"), name);
                } else {
-                       if (read_old_data(st, name, buf))
+                       if (read_old_data(st, name, buf, patch))
                                return error(_("failed to read %s"), name);
                }
        }
@@ -3432,7 +3456,7 @@ static int load_preimage(struct apply_state *state,
                /* We have a patched copy in memory; use that. */
                strbuf_add(&buf, previous->result, previous->resultsize);
        } else {
-               status = load_patch_target(state, &buf, ce, st,
+               status = load_patch_target(state, &buf, ce, st, patch,
                                           patch->old_name, patch->old_mode);
                if (status < 0)
                        return status;
@@ -3520,7 +3544,7 @@ static int load_current(struct apply_state *state,
        if (verify_index_match(ce, &st))
                return error(_("%s: does not match index"), name);
 
-       status = load_patch_target(state, &buf, ce, &st, name, mode);
+       status = load_patch_target(state, &buf, ce, &st, patch, name, mode);
        if (status < 0)
                return status;
        else if (status)

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