Revert "Removing the baseDir from the entry points, now that the full path is resolved"

This reverts commit a565a9dbbd07338eea2a8db55f7da08a534b9270.
Removing a method on the ActivityInterface that wasn't being read
Fixing and clarifying a problem with resolved and non-resolved paths

Primarily, the "skeletons" key on Activity is almost not needed. We don't actually read the skeleton files (because
the user is submitting his/her answers for the skeletons) so we only have them in Activity so that we can have some
extra validation that input files and contexts are included in the allowed set of files.

Related to this, almost none of the paths on Activity need to be resolved to their absolute location. Most (i.e. the
input files) just contain the actual, submitted contents. There are just a few things that are not submitted (context,
suite) where we need to have the absolute path so we can go find these files. This removes the resolving of the path
for skeleton files and for the entry point.
Adding a comment
Catching an edge case where a process fails, but there is no stderr

An example is if the entry point doesn't exist - the "Cannot open input file: index.php" is sent to stdout
Minor simplification to the PhpAwareSuite
Removing a property that does not appear to be used
Working to simplify the testing process

This introduces an ActivitySuiteInterface, with a runTest method, which is passed
an object. The idea is that we could hopefully have some real phpunit tests in the
suite to test that different variations are working/not working. This makes the
suite class a lot more re-usable. We haven't fully realized this yet, but that's the plan.
Removing some functions to make Result simpler