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The synchronization algorithm is in SparkleLib/Cmis.
CmisSync uses an SQLite database to cache checksums, server-side modification dates, etc, in CmisDatabase.cs.
The source code contains a lot of comments so it should be explicit. Please let us know if something is lacking.
The UI is based on SparkleShare, an excellent Git-synchronization tool. That explains why you might find references to SparkleShare in the source code.