On the “dead” file issue, I just posted a How-To topic on finding dead files with external tools (wget/diff).
Linting/proofing/validating Jekyll’s output can be complex and often requires site-by-site configuration, so I think it is best left to external tools or plugins.
A lot of Jekylers use html-proofer to check for broken links. Dead file checking would be a good fit for html-proofer, since it is just the inverse of link-checking. It might be possible to implement it as an html-proofer plugin, etc.