Some suggestions

Here are a few things I found confusing as I went through the user guide:

- On this page: https://www.commonwl.org/user_guide/07-containers/index.html
it's confusing that the hello.js file is made on the command line, while other files are copy+paste. I think this shows up on other pages as well. I was wondering where the `hello.js` file came from since all the other files I made manually. I think it would be easier for the user to follow if this was consistent.

- the same page says "`baseCommand: node` tells CWL that we will be running this command in a container". This confused me. Is "node" some kind of special command? Does that mean you can't have a native command named 'node' ? How exactly does that tell CWL that we will be running this in a container? Why doesn't CWL us the DockerRequirement hint/requirement to tell if it's running in a container, and how would you run a different command in a container?

- The example tool here: (https://www.commonwl.org/user_guide/17-metadata/index.html) is running `wc -l` on a binary file (bam format), which doesn't make sense. maybe this is just a non-working example, but still, it would be nice if the examples made sense

Start with the user guide's 07-containers page and its hello.js example, then review the 17-metadata example linked in the issue. Make file-creation instructions consistent, clarify how baseCommand relates to containers and DockerRequirement, and ensure the bam example is meaningful or replaced.

Written by the indexing model from the issue text.