include all source files in the report

hidden behind the --include-all-sources flag

After the coverage report has been built, manually instrument the files
which have not been visited already, and add those to the report.

When instrumenting the code manually, reset the count in the coverState
object. FunctionDeclaration is given a visit number of 1 when
instrumenting to compensate for function hoisting. We don't want that
in this case, as the file was not actually loaded.
add test for includeAllSources
do not reinstantiate transformer and instrumenter
assert that the default value for includeAllSources is set as expected
remove preload-sources option and add deprecation warning.
Merge pull request #275 from gustavnikolaj/feature/includeAllNonExcludedFilesInReport

Include all source files in the report
Add test for deprecation message, istanbul help config suppresses back-compat attributes
Update changelog, version, reconcile contributors
Merge https://github.com/gotwarlost/istanbul

Conflicts:
	package.json
add coffee support