Removed duplicate breakpoints.  Some refactoring.

Regardless of how users pass input, only one breakpoint will be generated per command in each file, keeping the report of commands analyzed accurate and the output cleaner (no duplicate lines for the same command in the report.)

Renamed -Coverage parameter on Invoke-Pester to -CodeCoverage.  I'm still not sure if that's the right name, but it'll do for now.  Also renamed -InputObject parameter on Enter-CoverageReport to -CodeCoverage as well, and removed pipeline input from Enter-CoverageReport. (It wasn't being used anyway.)  While making these changes, also extracted some code from a couple of longer functions into their own functions.
Removed some unnecessary comments, added documentation

There were a few comments added with the Isolation branch which are not really needed, so I took them out to reduce clutter.

Added documentation to Invoke-Pester's comment-based help around the new CodeCoverage parameter.