Added cmake build files for the conformance test runner.

Add contributing guidelines.

* Fix well known type class not inheriting Message

Previously, well known types only implement Message interface but not inhert it.
Fix the problem by calling zend_do_inheritance

* Add back commented tests

* Add missing reference to conformanc_test_impl.cc in Makefile

* Update conformance failure list

update version

Request new option extension (and update URLs for existing projects)

Update options.md | fix website url for C# port

Update my projects' (DCCL / Goby) URLs.
Propose new extension for CGSN Mooring project.

I want to use the conformance tests from upb, which is switching
to CMake.

Update options.md | fix website url for C# port of protocol buffers.. From `http://github.com/jskeet/dotnet-protobufs` to `https://github.com/jskeet/protobuf-csharp-port`

Revert changed links in Dockerfiles.

These changes require building new docker images and without new images
our kokoro tests are all failing.

Replace repo links.

Related to #658 and #5007.

Fix TryCreateParentDirectory on Windows

Change deprecated Bazel single file attr param

This removes the need for --incompatible_disable_deprecated_attr_params
when using Protobuf

* _SURROGATE_PATTERN check for ucs4
Skip some test for ucs2 by sys.maxunicode

Document wrapper non-uses

Document the cases where the wrapper well-known types are not useful.

Fix issues discovered in up-integration.

Add status badge for bazel build.

Fix bazel test.

* Fixes https://github.com/google/protobuf/issues/5031
* Fixes https://github.com/google/protobuf/issues/5037

Down-integrate proto2 namespace fix.

Fix json parsing of wrapper values

Add JS and Protobuf.js benchmark, fix js's reader.skipGroup

1. Fix C++ tests.
  * Add missing files to Makefile.am and fix distcheck in tests.sh
  * Remove BUILT_SOURCES from conformance/Makefile.am.
  * Add some missing override keyword.
  * Add a type cast to int64 because our StrCat() in stubs can't handle size_t.
2. Fix Java tests.
  * Add missing test dependency on guava in pom.xml.
  * Include newly referenced test data in test resources.
  * Manually fix map_lite_test.proto which is overwritten because it's mapped
    from map_test.proto in google3.
  * Add back "optimize_for = LITE_RUNTIME" which is still needed to keep the
    opensource test passing as it's still running lite tests.
  * Add a type cast in newBuilder() because without it the code doesn't compile
    with openjdk javac 1.8 (the compiler can't figure if it's the right type
    due to complex generic typing).
3. Fix Python tests.
  * Remove/replace references to <hash_map>.
  * Suppress more warnings in setup.py.
  * Replace incorrect header inclusion for google/protobuf/proto_api.h.
  * Add strings::EndsWith to google/protobuf/stubs/strutil.h because it's
    referenced in the updated python C extension code.
  * Replace proto2 with google::protobuf. The proto2 name is leaked to
    opensource because we removed the subsitition rule for proto2 namespace
    but only fixed C++ source code and forgot to update python C extension code.