Plot summary with cover letter for publisher- what does that mean exactly?

Okay. I'm going to assume you haven't actually been talking TO an editor, just maybe reading their submission guidelines, since they do not already have a cover letter from you yet.

www.absolutewriter.com/forum

Go to this group. There are published writers, even editors and a few agents, who hang out there (only a few of us, that I know of, are on Y!A). They are a large and knowledgable group and very willing to give advice. Plus, there are likely members who have direct experience with the publisher you are dealing with, so they can advise you a lot better on what, specifically, the editor wants and whether or not they are a reputable company.

I usually provide a synopsis in my cover letter, and have only been asked once to provide a summary as a separate document. I have yet to submitt an entire manuscript with a cover letter, as those I have sent work to ask for sample chapters, and when they are interested, then the whole thing.

If I were to submitt to someone who makes a point of wanting the summary, cover letter, and full manuscript (as worded in you question), I'd probably make it a separate document.