Use git clean before installing via bundler

Need to expose generated protobuf C++ headers

Merge 3.1.x branch into master.

Declare all inputs of protoc action

ctx.executable.plugin must be in the inputs of protoc's action when using a plugin, otherwise the action will fail.

This bug has been hidden by a bug in Bazel: for every ctx.action, Bazel used to automatically add the runfiles of all executable inputs of the RULE instead of using the inputs of the specific ACTION. Consequently, we could get away with underspecifying the inputs of the action.

Fix MSVC build when HAVE_LONG_LONG is defined.

Merge 3.1.x branch into master.

Fix python_cpp test on Mac. Link staticly when building extension, so that the extension doesn't require installing protobuf library. (#2232)

* PHP: fix ZTS tsrm_ls errors

* Fix a few more macros

There seem to already be .proto files out there that have conflicting
enum names, which will not be able to build successfully for some
languages (like C#). To prevent this problem from spreading, let's make
it an error for proto3 but just issue a warning for proto2. This fixes
issue #2179.

Un-breaks users who have old generated code and upgrade
to the 3.1.0 release.

A bug was causing generated JSPB code with CommonJS-style imports to
refer incorrectly to nested messages from other .proto files. The
generated code would have things like "test_pb.InnerMessage" instead of
"test_pb.OuterMessage.InnerMessage". This commit fixes the problem by
correctly taking into account any message nesting.

Needed to pick up a Java dependency change and re-populate the offline
repo.

[skip ci]

"ps: StartFileDownload" is broken by a recent appveyor image update:
http://help.appveyor.com/discussions/problems/5308-ci-frequently-hangs-with-recent-image-update

Change-Id: Ia73aa8b12f77eb9bbec556a4c05310153aad97bf

Change-Id: I6a5078b6bcdf4637e11c1cb9da1f74298e6fc26e