We should compare filepath with excluded path using "starts-with" because the filepath may be a child of the excluded path

This makes the excludes array work when using -r
Adding test for fix

Without the fix, we get the following when running ./jsdoc -T:
    Failures:

    jsdoc/src/filter Filter isIncluded

      1) should be able to exclude descendants of excluded subdirectories
      Message:
        Expected 4 to be 2.
      Stacktrace:
        undefined

      2) should be able to exclude descendants of excluded subdirectories
      Message:
        Expected 1 to be -1.
      Stacktrace:
        undefined

      3) should be able to exclude descendants of excluded subdirectories
      Message:
        Expected 3 to be -1.
      Stacktrace:
        undefined

    Finished in 6.696 seconds
    849 tests, 2050 assertions, 3 failures

This test passes with the fix.
Merge pull request #617 from cdparks/fix-excludes

Fix for #616, making excluded-filepaths play nicely with -r