Here is a sample project, which may be defined in your .emacs file.
(setq muse-project-alist '(("Website" ("~/Pages" :default "index") (:base "html" :path "~/public_html") (:base "pdf" :path "~/public_html/pdf"))))
The above defines a project named "website", whose files are located in the directory ~/Pages. The default page to visit is index. When this project is published, each page will be output as HTML to the directory ~/public_html, and as PDF to the directory ~/public_html/pdf. Within any project page, you may create a link to other pages using the syntax ‘[[pagename]]’.
If you would like to include only some files from a directory in a Muse project, you may use a regexp in place of ~/Pages in the example.