Here you get JSONObject so change this line:

JSONArray jsonArray = new JSONArray(readlocationFeed); 

with following:

JSONObject jsnobject = new JSONObject(readlocationFeed);

and after

JSONArray jsonArray = jsnobject.getJSONArray("locations");
for (int i = 0; i < jsonArray.length(); i++) {
    JSONObject explrObject = jsonArray.getJSONObject(i);
}

Take a look at this tutorial. Also you can parse above json like :

JSONArray arr = new JSONArray(yourJSONresponse);
List<String> list = new ArrayList<String>();
for(int i = 0; i < arr.length(); i++){
    list.add(arr.getJSONObject(i).getString("name"));
}

The problem is not the JSONArray.toString(), as @Selvin mentioned.

From JSONArray source:

/**
 * Encodes this array as a compact JSON string, such as:
 * <pre>[94043,90210]</pre>
 */
@Override public String toString() {
    try {
        JSONStringer stringer = new JSONStringer();
        writeTo(stringer);
        return stringer.toString();
    } catch (JSONException e) {
        return null;
    }
}

/**
 * Encodes this array as a human readable JSON string for debugging, such
 * as:
 * <pre>
 * [
 *     94043,
 *     90210
 * ]</pre>
 *
 * @param indentSpaces the number of spaces to indent for each level of
 *     nesting.
 */
public String toString(int indentSpaces) throws JSONException {
    JSONStringer stringer = new JSONStringer(indentSpaces);
    writeTo(stringer);
    return stringer.toString();
}

The problem is that you need to convert your ChecklistAnswer to JSON object first for your JSONArray to work properly.

Again from Javadoc:

/**
 * A dense indexed sequence of values. Values may be any mix of
 * {@link JSONObject JSONObjects}, other {@link JSONArray JSONArrays}, Strings,
 * Booleans, Integers, Longs, Doubles, {@code null} or {@link JSONObject#NULL}.
 * Values may not be {@link Double#isNaN() NaNs}, {@link Double#isInfinite()
 * infinities}, or of any type not listed here.

...

Something like this:

ArrayList<String> jsonStringToArray(String jsonString) throws JSONException {

    ArrayList<String> stringArray = new ArrayList<String>();

    JSONArray jsonArray = new JSONArray(jsonString);

    for (int i = 0; i < jsonArray.length(); i++) {
        stringArray.add(jsonArray.getString(i));
    }

    return stringArray;
}

// you should probably mention what json library you use in your question
String[] cities = new String[cities.length()];
for (int i = 0; i<cities.length(); i++) {
    cities[i] = cities.getJsonObject(i).getString("name");
}

Use gson. It's got a much friendlier API than org.json.

Collections Examples (from the User Guide):

Gson gson = new Gson();
Collection<Integer> ints = Lists.immutableList(1,2,3,4,5);

//(Serialization)
String json = gson.toJson(ints); ==> json is [1,2,3,4,5]

//(Deserialization)
Type collectionType = new TypeToken<Collection<Integer>>(){}.getType();
Collection<Integer> ints2 = gson.fromJson(json, collectionType);
//ints2 is same as ints

Look like you want to store name and location in an array, if yes then

for(int i=0; i < jLocation.length(); i++){
    arr[0] = jLocation.getJSONObject(i).getString("name");
    arr[1] = jLocation.getJSONObject(i).getString("location");
} 

Note - This code assume that you only have one name and location. However I sugegst you to do something like below:

Create a Location class, e.g. below

public class Location {
    private String name;
    private String location;

    public Location(String name, String location) {
        this.name = name;
        this.location = location;
    }

    public String getName() {
        return name;
    }

    public String getLocation() {
        return location;
    }
}

Then use it like below:

public static void main(String[] args) {
        List<Location> locations = new ArrayList<Location>();

        for(int i=0; i < jLocation.length(); i++){
            String name = jLocation.getJSONObject(i).getString("name");
            String location = jLocation.getJSONObject(i).getString("location");

            locations.add(new Location(name, location));
        } 
    }

To have a string value inside your JSON array, you must remember to backslash escape your double-quotes in your Java program. See the declaration of s below.

String s = "[[\"110917       \", 3.0099999999999998, -0.72999999999999998, 2.8500000000000001, 2.96, 685.0, 38603.0], [\"110917    \", 2.71, 0.20999999999999999, 2.8199999999999998, 2.8999999999999999, 2987.0, 33762.0]]";

Your code in the main() method works fine. Below is just a minor modification of your code in the main() method.

System.out.println("String to Json Array Stmt");
JsonParser parser = new JsonParser();
JsonElement tradeElement = parser.parse(s);
JsonArray trade = tradeElement.getAsJsonArray();
System.out.println(trade);

Lastly, remember to prefix your statement "com.google.gson.*" with the keyword "import", as shown below.

import com.google.gson.*;

So I ended up getting it to work with these changes! I had never worked with JSON before this project and apparently I had it written wrong for what I was trying to do.

        JSONParser jsonParser2 = new JSONParser();
        try (FileReader reader = new FileReader("Locations.json")) {
            Object obj = jsonParser2.parse(reader);

            JSONArray locationsList = (JSONArray) obj;

            //Iterate over locations array
            locationsList.forEach(emp -> parseJSONLocations((JSONObject) emp, locations, objects));

        } catch (FileNotFoundException e) {
            System.out.println(e);
        } catch (IOException | ParseException e) {
            System.out.println(e);
        }

and then the method to add it all to a class was changed as such:

    private static void parseJSONLocations(JSONObject locations, Locations[] location, Objects[] object) {
        JSONObject locationObject = (JSONObject) locations.get("locations");
        String desc = (String) locationObject.get("description");
        String name = (String) locationObject.get("name");
        JSONArray objects = (JSONArray) locationObject.get("objects");

        Iterator<String> it = objects.iterator();
        List<Objects> objs = new ArrayList<>();
        while (it.hasNext()) {
            String mStr = it.next();
            for (Objects elm : object) {
                if (elm.getName().equals(mStr)) {
                    objs.add(elm);
                }
            }
        }

        JSONArray directions = (JSONArray) locationObject.get("directions");
        Map<String, String> map = new HashMap<>();
        Iterator<JSONObject> it2 = directions.iterator();
        while (it2.hasNext()) {
            JSONObject value = it2.next();
            map.put((String) value.get("direction"), (String) value.get("location"));
        }
        location[index2] = new Locations(desc, name, objs, map);
        index2++;
    }

But then I also had to change my JSON code, per jgolebiewski's suggestion:

[
    {
        "locations": {
            "description": "You look around the room and see you are in an empty room with 2 doors to the left and to the right. Knowing not how you got there, you decide to figure out how to escape and get back to your normal life.",
            "name": "start",
            "objects": [],
            "directions": [{
                    "direction": "right",
                    "location": "empty room1"
                }, {
                    "direction": "left",
                    "location": "dungeon"
                }]
        }
    },
    {
        "locations": {
            "description": "Inside this room it looks like some sort of dungeon with a cage in the middle and blood lining the wall and floor.",
            "name": "dungeon",
            "objects": ["map", "torch"],
            "directions": [{
                    "direction": "up",
                    "location": "hallway2"
                }, {
                    "direction": "down",
                    "location": "hallway1"
                }, {
                    "direction": "right",
                    "location": "start"
                }]
        }
    }
]

Thank you for this tutorial for helping as well: https://howtodoinjava.com/library/json-simple-read-write-json-examples/

For anyone else who might need this:

String jsonString = "[\"string1\",\"string2\",\"string3\"]";
ObjectMapper mapper = new ObjectMapper();
List<String> strings = mapper.readValue(jsonString, List.class);

Using a stream you could convert it like so:

String s = "[\"A\",\"B\",\"C\",\"D\",\"E\"]";
String[] arr = Arrays.stream(s.substring(1, s.length()-1).split(","))
                .map(e -> e.replaceAll("\"", ""))
                .toArray(String[]::new);

You could also use a JSON library (which might be the prefered way). For example using Jackson:

String s = "[\"A\",\"B\",\"C\",\"D\",\"E\"]";
ObjectMapper mapper = new ObjectMapper();
String[] arr = mapper.readValue(s, String[].class);

You have to use JsonArray instead of JsonObject[]. Sample code:

String json = "[{ " + 
              "    \"id\":\"XXXX-XXXX-XXXX-XXXX-XXXX\", " + 
              "    \"name\":\"Name\" " + 
              "},{ " + 
              "    \"id\":\"XXXX-XXXX-XXXX-XXXX-XXXX\", " + 
              "    \"name\":\"Name\" " + 
              "}]";
Gson gson = new Gson();
JsonArray array = gson.fromJson(json,JsonArray.class);
System.out.println(array);

Output:

[{"id":"XXXX-XXXX-XXXX-XXXX-XXXX","name":"Name"},{"id":"XXXX-XXXX-XXXX-XXXX-XXXX","name":"Name"}]

If you want to work with a JsonObject[] you could do something like this:

JsonArray array = gson.fromJson(json,JsonArray.class);
JsonObject[] objects = new JsonObject[array.size()];
for(int i=0;i<array.size();i++)
    objects[i] = array.get(i).getAsJsonObject();
for(JsonObject x : objects)
    System.out.println(x);

Output:

{"id":"XXXX-XXXX-XXXX-XXXX-XXXX","name":"Name"}
{"id":"XXXX-XXXX-XXXX-XXXX-XXXX","name":"Name"}