HTML5 Archetype generated application produces dozens of Warnings inside of JBDS 5

Warnings like the following
1) Invalid character used in text string (HTML5 form element & validation).
because there is a raw "&" that is not properly encoded for HTML - should be & I believe
2) Invalid location of tag (meta).
on index.jsp - the meta tag is in the body element, not the head element
3) Missing semicolon
on jquery .js files - minified js causes Eclipse some heartburn
4) The local variable X may not have been initialized
on jquery file