Build cleanup

[jeromesimeon]

Lots of development lead to a pretty unwieldy (and poorly) documented build process, along with inconsistent Makefiles, unclear directory structures, etc. Some improvements are badly needed. Among some of the most important ones:

• Cleanup and integrate the Java part of the build process (Provide a more unified build for Java-based code #53)
• Build query runners the same way we build other Java parts of the system
• Remove java libraries that have been checked out, pull them from maven like the rest of them (Remove committed jars in ./lib #63)
• Systematically build bin/qcertJS.js and make it independent from the native build for bin/qcert
• Properly handle dependency of OCaml code to Coq code (./ocaml/extracted) shouldn't be recreated unless the Coq code has changed)
• Automate and document the build process for the documentation (See also Documentation consolidation #68)
• Provide a proper make tests target (See also Automated testing #72)
• Update the documentation for the build process in README.md

[jeromesimeon]

I'm declaring this round of cleanup closed.