Replaced IPC::System::Simple and Net::OpenSSH with IPC::Open3 to eliminate CPAN dependency for multiple distros. Using open3 will also be used for local processes so it make sense to switch now.
Also stopped replacing FORMAT number which explains the large number of test log changes. FORMAT should change very rarely and cause test log failures when it does.
More separation of the protocol and remote layers than was done in issue #106.
Settings are passed to the remote via command-line parameters rather than in the protocol.
* 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.
1) Re-checksums files that have checksums in the manifest
2) Recopies files that do not have a checksum
3) Saves the manifest at regular intervals to preserve checksums
4) Unit tests for all cases (that I can think of)
