Recurse into subdirs when determining staleness

[pedro-w]

When the plugin checks if the goal is up-to-date or needs to run, it generates a file containing the options and the names+timestamps of all files in the source and target directories. It then compares this to the last-saved version to
determine if anything had changed. The generation did not recursively descend into the directories and therefore files could change without the plugin noticing that it needed to run.

Also added some comments to explain the existing code.

I did not add unit tests as the changed source file does not have a corresponding unit test files. I have run and tested this on Windows only.

This relates to issue #1324

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