* Major refactoring of the protocol layer to support this work.
* Fixed protocol issue that was preventing ssh errors (especially connect) from being logged.
On some systems the JSON->encode() function was adding a linefeed and on others it was not. This was causing regression test failures in in the test logs and may have also been inconvenient for users.
* Includes updating the manifest to format 4. It turns out the manifest and .info files were not very good for providing information. A format update was required anyway so worked through the backlog of changes that would require a format change.
* Multiple database versions are now supported in the archive. Does't actually work yet but the structure should be good.
* Tests use more constants now that test logs can catch name regressions.
