This will work for you :

ObjectMapper mapper = new ObjectMapper();
JsonNode root = mapper.readTree(json);
Map<String, String> map = new HashMap<>();
addKeys("", root, map, new ArrayList<>());

map.entrySet()
     .forEach(System.out::println);

private void addKeys(String currentPath, JsonNode jsonNode, Map<String, String> map, List<Integer> suffix) {
    if (jsonNode.isObject()) {
        ObjectNode objectNode = (ObjectNode) jsonNode;
        Iterator<Map.Entry<String, JsonNode>> iter = objectNode.fields();
        String pathPrefix = currentPath.isEmpty() ? "" : currentPath + "-";

        while (iter.hasNext()) {
            Map.Entry<String, JsonNode> entry = iter.next();
            addKeys(pathPrefix + entry.getKey(), entry.getValue(), map, suffix);
        }
    } else if (jsonNode.isArray()) {
        ArrayNode arrayNode = (ArrayNode) jsonNode;

        for (int i = 0; i < arrayNode.size(); i++) {
            suffix.add(i + 1);
            addKeys(currentPath, arrayNode.get(i), map, suffix);

            if (i + 1 <arrayNode.size()){
                suffix.remove(arrayNode.size() - 1);
            }
        }

    } else if (jsonNode.isValueNode()) {
        if (currentPath.contains("-")) {
            for (int i = 0; i < suffix.size(); i++) {
                currentPath += "-" + suffix.get(i);
            }

            suffix = new ArrayList<>();
        }

        ValueNode valueNode = (ValueNode) jsonNode;
        map.put(currentPath, valueNode.asText());
    }
}

For the json you gave the output will be :

name-items-name-1-2=2nditem
name-items-name-1-1=firstitem
name-items-stock-1-1=12
name-first-1=John
name-items-stock-1-2=23
company=John Company
name-last-1=Doe

Yes, the Jackson manual parser design is quite different from other libraries. In particular, you will notice that JsonNode has most of the functions that you would typically associate with array nodes from other APIs. As such, you do not need to cast to an ArrayNode to use. Here's an example:

JSON:

{
    "objects" : ["One", "Two", "Three"]
}

Code:

final String json = "{\"objects\" : [\"One\", \"Two\", \"Three\"]}";

final JsonNode arrNode = new ObjectMapper().readTree(json).get("objects");
if (arrNode.isArray()) {
    for (final JsonNode objNode : arrNode) {
        System.out.println(objNode);
    }
}

Output:

"One"
"Two"
"Three"

Note the use of isArray to verify that the node is actually an array before iterating. The check is not necessary if you are absolutely confident in your data structure, but it's available should you need it (and this is no different from most other JSON libraries).

Compare with name and update that json element.

Resource resource = new ClassPathResource("gateway-fields.json");  //read from json file
      JsonFactory jsonFactory = new JsonFactory();
      ObjectMapper objectMapper = new ObjectMapper(jsonFactory);

      JsonNode arrayNode = objectMapper.readTree(resource.getFile()).get("fields");

      if (arrayNode.isArray()) {
          for (JsonNode jsonNode : arrayNode) {
              String nameFieldNode = jsonNode.get("name").asText();    
              if("RefNo".equals(nameFieldNode)){
                     ((ObjectNode)jsonNode).put("name", "1112");
              }
          }
      }

You are parsing the JSON when Jackson is meant to do it for you. Don't do this to yourself.

One option is to create a DTO (Data Transfer Object) that matches the format of your JSON

class Root {
    private String message;
    private String cod;
    private int count;
    private List<City> list;
    // appropriately named getters and setters
}

class City {
    private long id;
    private String name;
    private Coordinates coord;
    private List<Weather> weather;
    // appropriately named getters and setters
}

class Coordinates {
    private double lon;
    private double lat;
    // appropriately named getters and setters
}

class Weather {
    private int id;
    private String main;
    private String description;
    private int temp;
    // appropriately named getters and setters
}

Then use an ObjectMapper and deserialize the root of the JSON.

ObjectMapper mapper = new ObjectMapper();
Root root = mapper.readValue(yourFileInputStream, Root.class);

You can then get the field you want. For example

System.out.println(root.getList().get(0).getWeather().get(0).getTemp());

prints

74

The alternative is to read your JSON in as a JsonNode and traverse it until you get the JSON element you want. For example

JsonNode node = mapper.readTree(new File("text.json"));
System.out.println(node.get("list").get(0).get("weather").get(0).get("temp").asText());

also prints

74

For Jackson 2+ (com.fasterxml.jackson), the methods are little bit different:

CopyIterator<Entry<String, JsonNode>> nodes = rootNode.get("foo").fields();

while (nodes.hasNext()) {
  Map.Entry<String, JsonNode> entry = (Map.Entry<String, JsonNode>) nodes.next();

  logger.info("key --> " + entry.getKey() + " value-->" + entry.getValue());
}