Bazel is changing the way the execution root is organized (see https://github.com/bazelbuild/bazel/issues/1681
for details) and this updates the protobuf path logic to work with both old
and new versions of Bazel.

Revert "Fix Timestamps with dates before the Unix epoch that contain fractional seconds."

Fix Timestamps with dates before the Unix epoch that contain fractional seconds.

The Timestamp proto does not allow for negative nanos fields, so the seconds must be shifted and
a positive nanos then applied.

Add a proto_lang_toolchain for Java

This allows easy use of Bazel's java_proto_library native rule.

Class deprecation support

Fixed "make distcheck" for the Autotools build

Fixes #2088.

We now have separate tests for netcoreapp and net45 to test the two branches here.
(netstandard10 doesn't have MemoryStream.GetBuffer)

Although most of this library doesn't have any async functionality,
this feels like a natural place to locally add it.

To make the test pass I needed to fix out-of-tree builds and update
EXTRA_DIST and CLEANFILES.

* fix int64 decoding

* fix int64 decoding + tests

* Fix generation of extending nested messages in JavaScript

* Added missing test8.proto to build

* A few more cases for binary conformance tests.

* over-encoded varints (encoded in more bytes than are necessary).
* truncated varints (>32 bits for 32-bit types).

* Fixed Python decoding bug with 32-bit varints.

* Fixed 1L -> 1LL for 32-bit platforms.

Fixed cross compilations with the Autotools build

Minor fix for autocreated object repeated fields and maps.

- If setting/clearing a repeated field/map that was objects, check the class
  before checking the autocreator.
- Just to be paranoid, don’t mutate within copy/mutableCopy for the autocreated
  classes to ensure there is less chance of issues if someone does something
  really crazy threading wise.
- Some more tests for the internal AutocreatedArray/AutocreatedDictionary
  classes to ensure things are working as expected.
- Add Xcode 8.2 to the full_mac_build.sh supported list.

Add link to Elm proto plugin

Fix include in auto-generated well_known_types_embed.cc

Removed arena_nc.cc and arena_nc_test.py

This test is undocumented and it looks like it has probably never
worked. Let's just remove it to tidy things up. This fixes issue #2515.

Pull request #2517 caused cross compilations to start failing, because
the js_embed binary was being built to run on the target platform
instead of on the build machine. This change updates the Autotools build
to use the AX_PROG_CXX_FOR_BUILD macro to find a suitable compiler for
the build machine and always use that when building js_embed.

Fix warning in compiler/js/embed.cc

Restore include style fix (e3da722b) that has been trampled by
auto-generation of well_known_types_embed.cc

embed.cc: In function ‘std::string CEscape(const string&)’:
embed.cc:51:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < str.size(); ++i) {
                                ^

Init index_in_metadata_ without condition

Eliminate redundant methods in C++ generated code for lite protos

Chromium MemorySanitizer (MSan) reports use-of-uninitialized-value
of index_in_metadata_ attribute from EnumGenerator class. Fix these
warnings by initializing these attributes without condition.

Added the support for class level deprecation which will in turn also deprecate any fields that are currently using that type

Added Bazel genrule for generating well_known_types_embed.cc

In pull request #2517 I made this change for the CMake and autotools
builds but forgot to do it for the Bazel build.