This change adds the `--in-place` switch to nyc instrument
If `--in-place` is specified, the output directory will be set to equal the input directory for the instrument command.
This has the effect of replacing any file in the input directory that should be instrumented, with its instrumented counterpart.
The command will throw an error if the --delete option is specified.
The only way to instrument in place is with the --in-place switch, setting the input and output directories to be the same will not work
If `--in-place` is set the instrument command ignores any output directory specified with the command
If `--in-place` is set the instrument command will disable the `--complete-copy` switch as it is unnecessary.

I've made a few small code improvements to the instrument command spec.
I've also added tests to the old integration tests folder, I figured I could put tests here for the time being before they get moved to the new tap format.

The instrument --in-place test now runs in a copy of the instrument in place test directory, this means that running tests locally doesn't change your local environment.