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To run BlockSync, assuming that JRE executables are in your path, run:
java -jar BlockSync.jar
This will provide you with the syntax to use the tool.

Example:

Let's say you want to push the changes to a virtual disk image from your local
computer to a remote server, whose hostname is Zeus.

First we'd connect to Zeus through ssh (or similar), and navigate to the
directory that BlockSync has been placed in. Assuming that Ubuntu.vdi is a disk
image in the same directory we'd run the following command:
java -jar BlockSync.jar -s Ubuntu.vdi

BlockSync will then sit idle until a connection is received. On our local
computer we'd open a terminal, and navigate to the directory that BlockSync has
been placed in. Assuming that Ubuntu.vdi is a disk image in the same directory
we'd run the following command:
java -jar BlockSync.jar -c Ubuntu.vdi Zeus -push

BlockSync will then compute the differences in the files, and transfer the
non-identical blocks from your local computer to the remote server. While
BlockSync is working it will output details on what it's doing on your local
computer. When the process has finished, BlockSync will close on your local
computer and the remote server.

If we wanted to reverse the process and pull the changes to a virtual disk image
from the remote server to your local computer, we'd run the following command:
java -jar BlockSync.jar -c Ubuntu.vdi Zeus -pull

CAUTION: Remember the phrase, measure it twice and cut it once. When working
with BlockSync, always be sure that you're specifying the correct file and the
correct direction for changes to be applied. If either parameter is incorrect,
data *will* be lost.
Source: README, updated 2014-10-23