throw IOException instead of InvalidProtocolBufferException when appropriate

JSON Conformance improvements

Fixed Python 3.x C++ build, and updated conformance failure lists.

Fix tests broken by the Java directory change.

"valueField": null

is parsed appropriately, i.e. that it remembers that the field is set.

Previously we were incorrectly packing wrapper types.
This also refactors FieldCodec a bit as well, using more C# 6-ness.

Change-Id: I39c4eadbd28164cfd83aa2d1d8b6dfe8286db803

Restructuring protobuf to multiple modules

protobuf/java will become a parent pom that will contain two modules:

core - contains all of the code for the protobuf-java artifact
util - contains all of the code for the protobuf-java-util artifact

Also cleaned up various Maven warnings.

- Spot an Any without a type URL
- In the conformance test runner, catch exceptions due to generally-invalid JSON

Prohibit null values in maps

Allow conformance test runner to tolerate crashes, and re-enable conformance tests

Fix typos in README.md/CHANGES.txt

Release the semaphore in dealloc, fixing leak.

Add the docs claimed define for HAVE_UNORDERED_MAP

On deserialization, missing values for message types
are replaced with a "default" message.