Add compatibility notice for Java.

Move test for standalone BoolValue to JsonParserTest

Fix C++ Boost incompatibility on Windows/MSVC

Also added a standalone formatter test, for confidence.
Have validated that undoing the change in 835fb947 breaks the tests
(i.e. we are still testing that the change is required).

Fix C# Json parsing of well-known type Boolvalue

Declare an init and avoid passing NULL to initWithValue:count:

Fixes https://github.com/google/protobuf/issues/1189

Build cleanup

Remove accidentally restored deleted files.

Fix the std::string error introduced in integration.

updated README

Updated README.md

- Fixes up `make distclean` and `make maintainer-clean`
- Fixes the build so make is more likely to notice if one of those files is stale/missing.

Added relative link to cmake guide.

Allow custom type URL prefixes in Any.Pack

Fix bug with silent message corruption in LITE_RUNTIME.

Properly generating well known proto files for the macos build.

Added framework for generating/consuming benchmarking data sets.

Few tweaks to the rakefile to permit native gems compilation with the proto files generation.

Merge Google internal changes

Fix cp -r usage to be portable.

cp -r foo/ bar/ in linux will create a bar/foo directoy. In the
objectivec generate descritpor case, well known types will be created in
objectivec/google/google/protobuf/.. if the command is run under linux.

Adding the trailing period fixes the behavior inconsistency.