Java 9 (to be released in 27 days) has removed tools.jar entirely. The documentation generation code in libsbml errors because it can't find tools.jar, in docs/CMakeLists.txt, around "Java_JAVADOC_JAR".
The classes that it depends on are deprecated, but are present in the Java 9 release: it may simply be a case of removing the error that the file isn't found.
Thank you very much for reporting this, and my apologies for the trouble this is causing.
This change in Java 9 is unfortunate, and it's going to be problematic because our document-generation chain relies on being able to use the javadoc functions that were in tools.jar.
I think this is the death knell for our use of javadoc for the libsbml docs. I think this is the final straw that says we'll have to generate docs using Doxygen only.
I can confirm now that under Java 9, it's not necessary to include the tools.jar to compile the SBMLDoclet.java file used by our documentation production scheme. I'm currently working on the changes needed to deal with that. Hopefully they will be in the upcoming next libSBML release.
This is (in principle) fixed in the source code base and will be in the next release. I'm going to close this issue. Thank you again for filing the report!