Support reporting within symlink/junction

This changes the matcher for source files to get the file list as
real paths (resolving links) such that when the matcher checks if
the file is covered from the Node.js core module path, it actually
matches, since it uses realpath.
Fix linting error in test-instrument-command
Move jshint config into a separate file

It seems better for clarity to store different things in different places.
package.json is already a big and complicated file, and .jshintrc is
a special file precisely for storing this configuration.

Not to mention that jshint authors themselves have switched away
from using jshintConfig key:
https://github.com/jshint/jshint/commit/91bf14ddc81821a54b711a06fe229f0b2427c8e6
Add per-file checks, configuration support, and CI fixes.
Merge pull request #268 from FormidableLabs/feature-per-file-coverage-final

Add per-file / config-based coverage enforcement.
Update changelog, add contributor, up version
Merge pull request #219 from dougwilson/fix/symlinks

Support reporting within symlink/junction
Update changelog, add contributor, up version
get rid of preferGlobal in package.json

closes #270
Merge pull request #258 from denis-sokolov/jshint-config

Move jshint config into a separate file
Merge pull request #280 from andrewrk/master

get rid of preferGlobal in package.json
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.