Some general comments:
1) I think a design document to explain what each class does and how they interact with each other is required. Other option is to create a package.html file and document design/code in place. I think the second option is better.
At the mininum, each class needs a detailed javadoc at the beginning and for each major method. Important and useful contribution like this may not get accepted if not documented properly.
2) Package location needs to be changed. All tools are in org.apache.derby.tools package. Best to follow existing tools like IJ, DBLOOK model so it would be easy to use and to enable derbyrun option for this tool later.
3) Looks like the code uses generics, which limit the use to JDK 1.5 platforms. While this may be ok, need to document need for JDK 1.5 platform and raise appropriate message if used in earlier platforms. Most of derby can still run on JDK 1.3 platforms, though not required for new indepedent modules.
4) There are many areas that need improvements in the code... like exception handling, importing only classes that are needed not the whole package, deleting code that is in comments etc. I understand the code is still in development.
I would like to suggest you focus on completing current functionality very well, document what you have done, move code and integrate it at appropriate location and test current functionality before adding more.
Better to submit partial code that is well written than submit more code that is not very usable.