Revert "Using the ClassLoader is important too"

This reverts commit 6624689cb6366f09c4106b100c0f5e63ac9c5375.
Revert "Restored the leading slash-less config file paths"

This reverts commit b13ba75b9bf94fb6c874290224f71463f9c4a27f.
Revert "moves MMFF94 parameter loading to a single (previously broken) method - resolves failing unit test"

This reverts commit 63e375742de8919197abc89449011bc7ea511bf2.
Revert "grouping location fields and correcting value (leading slash)"

This reverts commit 18b53bfecc0ab9e3a098c98f1e0f52f5b424acdc.
Revert "moved configuration of MM2 into a single (previously broken) method - resolves unit test in error"

This reverts commit 1b29ea854a55f6f225133818fad94e6772703a94.
Revert "removed settable input stream, this could be reintroduced but should be done via a constructor. the configFile path was corrected and renamed, several small tidy ups to the loading code"

This reverts commit c13cebea040928e3a543431ca94f41e0af3d030f.