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

- merge loop for .h and .proto includes
- fix shellcheck errors

For google/or-tools, on windows, we need to use `import "google/protobuf/wrappers.proto";` since we want "optional" int64 and in version3 POD get default value...
-> so we use "google.protobuf.Int64Value" since 0 is a valid value and different from "not set" for our use case.

This should fix Bazel builds, since those were missing a new file
(implicit_weak_message.cc).

- Removed the redefination in the atomicword_compat.h. Now Atomic32 will
alwyas be intptr_t in 32bit platforms, the bridge is no longer needed.
- Change NaCl 64bit to use intptr_t instead of int32 for Atomic32,
otherwise AtmoicWord APIs will miss the definations.

After this change, the AtmoicWord will always be either Atomic32 or
Atmoic64 depending on the platforms.

Add implementations of open(2), mkdir(2), stat(2),
etc. that support long paths under Windows (paths
longer than MAX_PATH in <windows.h>, which is 260
characters).

The implementations are in a separate namespace
(google::protobuf::internal::win32), so they won't
collide with the standard implementations in
<io.h>, but after importing them with `using` they
can be drop-in replacements.

Fixes https://github.com/bazelbuild/bazel/issues/2634
Fixes https://github.com/google/protobuf/issues/2891

install 'generated_message_table_driven.h' and 'metadata_lite.h', they are included when compiling the files generated using protoc.exe 3.3.0

This allows the file path to contain spaces which is very common on
windows.

the deprecated atomics.

This is necessary so that the CMake build knows to include this header
file in the installation include/ directory.

This is necessary so that the CMake build knows to include this header
file in the installation include/ directory.

This pull request includes two implementation: C extension and PHP
package. Both implementations support encode/decode of singular,
repeated and map fields.

* `csharp_options`: Added `Options` to encapsulate generator options.
   Supported options for now - file_extension, base_namespace
* `{Blah}Generator`: Now accept `Options*` as parameter to constructor
* `csharp_generator.cc`: Parse and populate options
* `Makefile.am`: Added `csharp_options.h`
* `extract_includes.bat.in`: Added `csharp_options.h`

Refactoring code to two commits. This is the first commit

Change-Id: I6fa9f1b65d6c06b891aabf3f3d868364d74d727d

Change-Id: Ieb7a2c2fbf35bc2a8fa65b915a5ecb68c83863e4

Change-Id: I75459b8b6562c3ac58fa4b1e4513accdda43ad64

Change-Id: Ifbc415755266ba3d0ffa5661fcd7c7d2e3b32a22