Path Clarity changes and dependency updates

[giarc3]

I couldn't write/review any more documentation today, so I took a small tech debt issue

• Rename/move files so we don't have to have anything named mod.rs (see attached issue for a diagram of how the new structure works)
• Remove all extern_crate from lib.rs and instead import things directly where they're needed
• Upgrade dependencies
  • protobuf-codegen-pure needed some changes in build.rs
  • percent-encoding needed some changes in src/internal/rest.rs. I could use a double-check on this one, so I would recommend viewing the single commit where I upgraded it to review.

[clintfred]

Not sure if this warrants a "Notable Internal Changes" changelog entry, but maybe...