InputStream is = entity.getContent();
String filePath = "sample.txt";
FileOutputStream fos = new FileOutputStream(new File(filePath));
int inByte;
while((inByte = is.read()) != -1)
     fos.write(inByte);
is.close();
fos.close();

EDIT:

you can also use BufferedOutputStream and BufferedInputStream for faster download:

BufferedInputStream bis = new BufferedInputStream(entity.getContent());
String filePath = "sample.txt";
BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(new File(filePath)));
int inByte;
while((inByte = bis.read()) != -1) bos.write(inByte);
bis.close();
bos.close();

You can get the file name and extension from your response's content-disposition header

First get the header then parse it for the filename as explained here, i.e:

HttpEntity entity = response.getEntity();
if (entity != null) {
    String name = response.getFirstHeader('Content-Disposition').getValue();
    String fileName = disposition.replaceFirst("(?i)^.*filename=\"([^\"]+)\".*1");
    FileOutputStream fos = new FileOutputStream("C:\\" + fileName);
    entity.writeTo(fos);
    fos.close();
}

Oh my god I finally got something that worked. Ok. So apparently HTTPClient can only handle 2 responses before it starts to bug out, according to here: Why does me use HttpClients.createDefault() as HttpClient singleton instance execute third request always hang

So instead, I changed my code to just get a login response, then get the excel file as a response and then quit. I also added some timeout configurations and also changed order from Exporting the file first and then Consuming the entity. I used a separate 2nd response and 2nd entity. That seemed to have helped a bit too? I'm guessing.

import java.util.List;
import java.util.ArrayList;
import org.apache.http.*;
import java.io.*;

import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.CookieStore;
import org.apache.http.client.config.CookieSpecs;
import org.apache.http.client.config.RequestConfig;
import org.apache.http.client.methods.*;
import org.apache.http.client.protocol.HttpClientContext;
import org.apache.http.conn.ConnectionPoolTimeoutException;
import org.apache.http.cookie.Cookie;
import org.apache.http.impl.client.*;
import org.apache.http.message.*;
import org.apache.http.util.EntityUtils;
import org.apache.http.client.entity.*;

public class hcFeb {
    public static void main (String[] args) throws ClientProtocolException, IOException {
        //Set up Cookie settings and also Timeout settings
        CookieStore cookieStore = new BasicCookieStore();
        HttpClientContext context = HttpClientContext.create();
        context.setCookieStore(cookieStore);
        
        int CONNECTION_TIMEOUT = 80000;
        RequestConfig requestConfig = RequestConfig.custom().setCookieSpec(CookieSpecs.DEFAULT)
                .setConnectionRequestTimeout(CONNECTION_TIMEOUT)
                .setConnectTimeout(CONNECTION_TIMEOUT)
                .setSocketTimeout(CONNECTION_TIMEOUT)
                .build();
        
        //Set up HttpClient
        CloseableHttpClient httpclient = HttpClients.custom().setDefaultRequestConfig(requestConfig).setDefaultCookieStore(cookieStore).disableContentCompression().build();
        
        HttpGet httpGet = new HttpGet("http://website");
        CloseableHttpResponse response = httpclient.execute(httpGet);
        
        //Create Post request to log into the website
        HttpPost httpPost = new HttpPost("http://loginwebsite");
        
        //Login to website
         List <NameValuePair> nvps = new ArrayList <NameValuePair>();

            nvps.add(new BasicNameValuePair("user","username"));
            nvps.add(new BasicNameValuePair("password","password"));
            nvps.add(new BasicNameValuePair("button", "Login"));
            nvps.add(new BasicNameValuePair("task", "extlogin"));
            httpPost.setEntity(new UrlEncodedFormEntity(nvps));
            response = httpclient.execute(httpPost);

        
        try{
            System.out.println(response.getStatusLine());   
            HttpEntity entity = response.getEntity();
            EntityUtils.consume(entity);                
        } finally{
        }
        
        //Send request for Excel file and download it.
        String link = "http://website.com/uri?ActSts=Edit&task=filter&Field=Plant";
        HttpGet get = new HttpGet(link);
        
        //maybe create new response
        HttpResponse response2;

        try{
            response2 = httpclient.execute(get,context);
            System.out.println(response2.getStatusLine());  
            HttpEntity entity1 = response2.getEntity();


            if (entity1 != null) {
                System.out.println("Entity isn't null");
                
                InputStream is = entity1.getContent();
                String filePath = "C:\\Users\\windowsUserName\\Downloads\\WODETAIL_List.xls";
                FileOutputStream fos = new FileOutputStream(new File(filePath));
                
                byte[] buffer = new byte[5600];
                int inByte;
                while((inByte = is.read(buffer)) > 0)
                    fos.write(buffer,0,inByte);
                is.close();
                fos.close();
                
                System.out.println("Excel File recieved");                  
                
                
                EntityUtils.toString(response2.getEntity());
                EntityUtils.consume(entity1);
                
            }
            
        } catch (ConnectionPoolTimeoutException e){
            //response.close();
            System.out.println(e.getMessage());
        } catch (IOException e){
            System.out.println(e.getMessage());
        }
        
    }
}

Your url (when set to correct github repos) may be returning redirect status 302. To make HTTP client follow redirects replace HttpClient client = HttpClient.newHttpClient() with use of HttpClient.newBuilder(). You can also simplify your code with try with resources and making use of InputStream.transferTo:

HttpClient client = HttpClient.newBuilder().followRedirects(Redirect.ALWAYS).build();

URI uri = URI.create("https://api.github.com/repos/:owner/:repo/zipball/:ref");
HttpRequest request = HttpRequest.newBuilder().uri(uri).build();

// use the client to send the asynchronous request
InputStream is = client.sendAsync(request, BodyHandlers.ofInputStream())
        .thenApply(HttpResponse::body).join();
try (FileOutputStream out = new FileOutputStream("outputZipFile.zip")) {
    is.transferTo(out);
}

Using httpclient is pretty easy. Here's a link to it's tutorial.

http://hc.apache.org/httpcomponents-client-ga/tutorial/html/fundamentals.html#d5e43

HttpClient httpclient = new DefaultHttpClient();
HttpGet httpget = new HttpGet(urltofetch);
HttpResponse response = httpclient.execute(httpget);
HttpEntity entity = response.getEntity();
if (entity != null) {
    long len = entity.getContentLength();
    InputStream inputStream = entity.getContent();
    // write the file to whether you want it.
}