> So even if one was to not use it in embedded mode,
> my question is still whether the Jaybird JAR file
> is a total re-write of Firebird database engine in Java
> hence it is all in this file.

No, it is not. jaybird-x.x.x-full.jar is a JAR that contains also
dependent libraries for those that have simple setup, want to take a jar
file and do not bother themselves with other dependencies. Can lead to
lib conflicts.

> OR is is just a driver to connect to the FireBird engine
> which is just a ".dll" file.

In order to use fbembed.dll you need jaybird-x.x.x.jar and jaybirdXX.dll.

> Once again I wish to know what files
> are important to just get started.

What about reading "Distribution package" chapter from release notes
(page 8 in PDF)?

Also you can check "Using Type 2 and Embedded Server driver" in release
notes (beginning from page 11 in PDF) - if there are unclear parts,
please ask questions here and/or help to formulate them better.

Roman