Add .PHONY entries, add *.cpp dependencies for binary targets

[linuxkidd]

This update helps normalize the Makefile(s) for better user experience.

Specifically:

• Targets that do not create a file with the name of the target are labeled .PHONY per Makefile spec
• Targets which do compile a source have that source listed as a dependency - this permits updates to the source to be noticed and re-compiled on the next make call.

This may resolve make deps issue from #590

[ckuethe]

Doesn't break on my machine. :)