bugfix: modifying the Cookie request headers via ngx.req.set_header or ngx.req.clear_header did not update the Nginx internal data structure, r->headers_in.cookies, at the same time, which might cause issues when reading variables $cookie_COOKIE, for example. thanks Matthieu Tourne for the patch.

ngx-lua-set-cookie-header.patch

diff --git a/src/ngx_http_lua_headers_in.c b/src/ngx_http_lua_headers_in.c
index 9987e54..8391de0 100644
--- a/src/ngx_http_lua_headers_in.c
+++ b/src/ngx_http_lua_headers_in.c
@@ -29,6 +29,8 @@ static ngx_int_t ngx_http_set_connection_header(ngx_http_request_t *r,
     ngx_http_lua_header_val_t *hv, ngx_str_t *value);
 static ngx_int_t ngx_http_set_content_length_header(ngx_http_request_t *r,
     ngx_http_lua_header_val_t *hv, ngx_str_t *value);
+static ngx_int_t ngx_http_set_cookie_header(ngx_http_request_t *r,
+    ngx_http_lua_header_val_t *hv, ngx_str_t *value);
 static ngx_int_t ngx_http_clear_builtin_header(ngx_http_request_t *r,
     ngx_http_lua_header_val_t *hv, ngx_str_t *value);
 static ngx_int_t ngx_http_clear_content_length_header(ngx_http_request_t *r,
@@ -103,6 +105,10 @@ static ngx_http_lua_set_header_t  ngx_http_lua_set_handlers[] = {
                  offsetof(ngx_http_headers_in_t, content_length),
                  ngx_http_set_content_length_header },
 
+    { ngx_string("Cookie"),
+                 0,
+                 ngx_http_set_cookie_header },
+
 #if (NGX_HTTP_REALIP)
     { ngx_string("X-Real-IP"),
                  offsetof(ngx_http_headers_in_t, x_real_ip),
@@ -401,6 +407,45 @@ ngx_http_set_content_length_header(ngx_http_request_t *r,
 
 
 static ngx_int_t
+ngx_http_set_cookie_header(ngx_http_request_t *r,
+    ngx_http_lua_header_val_t *hv, ngx_str_t *value)
+{
+    ngx_table_elt_t  **cookie, *h;
+
+    if (!hv->no_override && r->headers_in.cookies.nelts > 0) {
+        ngx_array_destroy(&r->headers_in.cookies);
+
+        if (ngx_array_init(&r->headers_in.cookies, r->pool, 2,
+                           sizeof(ngx_table_elt_t *))
+            != NGX_OK)
+        {
+            return NGX_ERROR;
+        }
+
+        dd("clear headers in cookies: %d", (int) r->headers_in.cookies.nelts);
+    }
+
+    if (ngx_http_set_header_helper(r, hv, value, &h, 0) == NGX_ERROR) {
+        return NGX_ERROR;
+    }
+
+    if (value->len == 0) {
+        return NGX_OK;
+    }
+
+    dd("new cookie header: %p", h);
+
+    cookie = ngx_array_push(&r->headers_in.cookies);
+    if (cookie == NULL) {
+        return NGX_ERROR;
+    }
+
+    *cookie = h;
+    return NGX_OK;
+}
+
+
+static ngx_int_t
 ngx_http_clear_content_length_header(ngx_http_request_t *r,
     ngx_http_lua_header_val_t *hv, ngx_str_t *value)
 {
diff --git a/t/113-req-header-cookie.t b/t/113-req-header-cookie.t
new file mode 100644
index 0000000..5265860
--- /dev/null
+++ b/t/113-req-header-cookie.t
@@ -0,0 +1,251 @@
+# vim:set ft= ts=4 sw=4 et fdm=marker:
+
+use lib 'lib';
+use Test::Nginx::Socket;
+
+#worker_connections(1014);
+#master_process_enabled(1);
+#log_level('warn');
+
+repeat_each(2);
+
+plan tests => repeat_each() * (4 * blocks());
+
+#no_diff();
+no_long_string();
+
+run_tests();
+
+__DATA__
+
+=== TEST 1: clear cookie (with existing cookies)
+--- config
+    location /t {
+        rewrite_by_lua '
+           ngx.req.set_header("Cookie", nil)
+        ';
+        echo "Cookie foo: $cookie_foo";
+        echo "Cookie baz: $cookie_baz";
+        echo "Cookie: $http_cookie";
+    }
+--- request
+GET /t
+--- more_headers
+Cookie: foo=bar
+Cookie: baz=blah
+
+--- stap
+F(ngx_http_lua_rewrite_by_chunk) {
+    printf("rewrite: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+F(ngx_http_core_content_phase) {
+    printf("content: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+--- stap_out
+rewrite: cookies: 2
+content: cookies: 0
+
+--- response_body
+Cookie foo: 
+Cookie baz: 
+Cookie: 
+
+--- no_error_log
+[error]
+
+
+
+=== TEST 2: clear cookie (without existing cookies)
+--- config
+    location /t {
+        rewrite_by_lua '
+           ngx.req.set_header("Cookie", nil)
+        ';
+        echo "Cookie foo: $cookie_foo";
+        echo "Cookie baz: $cookie_baz";
+        echo "Cookie: $http_cookie";
+    }
+--- request
+GET /t
+
+--- stap
+F(ngx_http_lua_rewrite_by_chunk) {
+    printf("rewrite: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+F(ngx_http_core_content_phase) {
+    printf("content: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+--- stap_out
+rewrite: cookies: 0
+content: cookies: 0
+
+--- response_body
+Cookie foo: 
+Cookie baz: 
+Cookie: 
+
+--- no_error_log
+[error]
+
+
+
+=== TEST 3: set one custom cookie (with existing cookies)
+--- config
+    location /t {
+        rewrite_by_lua '
+           ngx.req.set_header("Cookie", "boo=123")
+        ';
+        echo "Cookie foo: $cookie_foo";
+        echo "Cookie baz: $cookie_baz";
+        echo "Cookie boo: $cookie_boo";
+        echo "Cookie: $http_cookie";
+    }
+--- request
+GET /t
+--- more_headers
+Cookie: foo=bar
+Cookie: baz=blah
+
+--- stap
+F(ngx_http_lua_rewrite_by_chunk) {
+    printf("rewrite: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+F(ngx_http_core_content_phase) {
+    printf("content: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+--- stap_out
+rewrite: cookies: 2
+content: cookies: 1
+
+--- response_body
+Cookie foo: 
+Cookie baz: 
+Cookie boo: 123
+Cookie: boo=123
+
+--- no_error_log
+[error]
+
+
+
+=== TEST 4: set one custom cookie (without existing cookies)
+--- config
+    location /t {
+        rewrite_by_lua '
+           ngx.req.set_header("Cookie", "boo=123")
+        ';
+        echo "Cookie foo: $cookie_foo";
+        echo "Cookie baz: $cookie_baz";
+        echo "Cookie boo: $cookie_boo";
+        echo "Cookie: $http_cookie";
+    }
+--- request
+GET /t
+
+--- stap
+F(ngx_http_lua_rewrite_by_chunk) {
+    printf("rewrite: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+F(ngx_http_core_content_phase) {
+    printf("content: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+--- stap_out
+rewrite: cookies: 0
+content: cookies: 1
+
+--- response_body
+Cookie foo: 
+Cookie baz: 
+Cookie boo: 123
+Cookie: boo=123
+
+--- no_error_log
+[error]
+
+
+
+=== TEST 5: set multiple custom cookies (with existing cookies)
+--- config
+    location /t {
+        rewrite_by_lua '
+           ngx.req.set_header("Cookie", {"boo=123","foo=78"})
+        ';
+        echo "Cookie foo: $cookie_foo";
+        echo "Cookie baz: $cookie_baz";
+        echo "Cookie boo: $cookie_boo";
+        echo "Cookie: $http_cookie";
+    }
+--- request
+GET /t
+--- more_headers
+Cookie: foo=bar
+Cookie: baz=blah
+
+--- stap
+F(ngx_http_lua_rewrite_by_chunk) {
+    printf("rewrite: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+F(ngx_http_core_content_phase) {
+    printf("content: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+--- stap_out
+rewrite: cookies: 2
+content: cookies: 2
+
+--- response_body
+Cookie foo: 78
+Cookie baz: 
+Cookie boo: 123
+Cookie: boo=123; foo=78
+
+--- no_error_log
+[error]
+
+
+
+=== TEST 6: set one custom cookie (without existing cookies)
+--- config
+    location /t {
+        rewrite_by_lua '
+           ngx.req.set_header("Cookie", {"boo=123", "foo=bar"})
+        ';
+        echo "Cookie foo: $cookie_foo";
+        echo "Cookie baz: $cookie_baz";
+        echo "Cookie boo: $cookie_boo";
+        echo "Cookie: $http_cookie";
+    }
+--- request
+GET /t
+
+--- stap
+F(ngx_http_lua_rewrite_by_chunk) {
+    printf("rewrite: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+F(ngx_http_core_content_phase) {
+    printf("content: cookies: %d\n", $r->headers_in->cookies->nelts)
+}
+
+--- stap_out
+rewrite: cookies: 0
+content: cookies: 2
+
+--- response_body
+Cookie foo: bar
+Cookie baz: 
+Cookie boo: 123
+Cookie: boo=123; foo=bar
+
+--- no_error_log
+[error]
+