This allows you to better select which files are instrumented when running the instrument command.  It's a pretty minimal implementation to make it as easy as possible to integrate with other proposed changes.  Test support is included with this change.

# Conflicts:
#	lib/commands/instrument.js

# Conflicts:
#	lib/commands/instrument.js

# Conflicts:
#	index.js
#	lib/commands/instrument.js
#	test/nyc-integration.js

…nstrumented versions where needed

So I've implemented this using `fs-extra`, not sure if that's the module you wish to go with here.
This is now relying on `testExclude.globSync` to get the correct files for instrumentation, so no more `shouldInstrument`
There's quite a few test changes in here, as `fs-extra.copySync` won't let you copy from `./` to `./outputMkdirHere`, but they're probably for the best anyway.
This also means that any attempt to store the instrumentation result in a subdir of the input dir will fail.

…o `output` dir

It ignores files in the `.git` folder and copies empty directories
Unfortunately I had to keep `fs-extra`, although this should be easy to drop when the project moves to node 8+ when `fs.copyFileSync` is made available.
We need to use `fs.chmodSync` to set the mode as any `write` mode flags get filtered when trying to set them through `fs.writeFileSync`.

What's missing?
 * No check to see where the working directory is relative to the project root directory
 * Tests confirming includes/excludes can be set in a config file or stanza and are observed by the instrument command
 * Tests confirming file permissions match between files in the input and output directories
 * Tests confirming we can't instrument outside of the project root directory

…tside of cwd

Tests include
  * using a `.nycrc` file to specify excludes
  * checking that file mode is preserved after instrumentation,
  * copying all uninstrumented files across to the output directory
  * Ensure that we can't instrument in place, overwriting the existing source
  * Ensure that we can't instrument source from outside the project root directory

A file `node_modules` file involved in the tests was being git ignored

# Conflicts:
#	index.js

In the last attempt at this I was jumping through hoops trying to maintain empty folders and structure etc.  Turns out none of that is necessary.
So this change runs the instrumentation process over the included files, then copies across anything remaining excluding freshly created output directory.

And a test to prove it!

…ude`

Previously this was adding `nyc instrument` full copy of `src` to `dst` as well as `include`/`exclude`
The full copy work was proving troublesome so it's been moved to it's own branch/PR
This commit removes the full copy, removes now unused dependencies, and updates tests accordingly