Some enhancements to the msvs-ninja integration

As a follow up to r1618, these are some changes that make the generated msvs
projects easier to work with:

* Fix the SHARED_INTERMEDIATE_DIR variable to point to ninja's intermediate
  directory. This is only done if we are using the ninja flavor explicitly.

* Add rule files to sources. Previously, these files were not showing up in the
  project because they get added in the rule generation step, which we skip
  when using an external builder.

* Do not put action/rule inputs in 'excluded_sources'. Since we are using an
  external builder, we don't need to "exclude" these files from the build. With
  this change, these files show up in their proper source heirarchy, instead of
  a separate "_excluded_files" folder. Also, these files also now show up even
  when "msvs_list_excluded_files" is used.

BUG=
R=scottmg@chromium.org

Review URL: https://codereview.chromium.org/16784002

git-svn-id: http://gyp.googlecode.com/svn/trunk@1653 78cadc50-ecff-11dd-a971-7dbc132099af