This behavior may be intended (if so, ignore...), but I was pretty confused by it when trying out the tools, so I wanted to bring it up anyway.

I ran the following command to compare two of the example documents:

$ java -jar tools-java-1.1.0-jar-with-dependencies.jar CompareDocs compareOutput.xlsx ../testResources/SPDXJSONExample-v2.2.spdx.json ../testResources/SPDXJSONExample-v2.3.spdx.json

In the resulting spreadsheet, the two names were shown as 2.spdx.json and 3.spdx.json; the common part in the beginning was most likely trimmed by the normalizeDocNames function.