I use the zip tool a lot in Ubuntu 14.04 and 16.04 because I work with people who use Windows. I also use tar, but we can talk about that in another tutorial.
Here's the command to create a zip file of your current working directory, including all files and folders:
zip -r FILE.zip .
Note: Don't forget the "." at the end.
Here's an example. We'll pretend we're working on a site called Web App Path, so we're going to call our zip file wap.zip.
Here's how you can make a zip archive called wap.zip:
zip -r wap.zip .
Sometimes, though, you need to make a zip file that doesn't include a folder. For instance, if you use NetBeans, there is often a folder called nbproject in your project directory. Here's how you can exclude that folder via the command line:
zip -r wap.zip . -x nbproject/\*
There is a lot more to the zip tool, but this is basically all I ever do with it.