Java Documentation

I need to document a Java project. I am a C # programmer and systems analyst. But I'm new to Java.

I have directories extracted from SVN.

These directories include source directories, WEB-INF, and other files needed to define the project, classpath, etc.

I understand that files essentially fall into one of the following three categories

• Source Code Files / Directories Based on Package Structuring Method (.Java)
• Directories / Files necessary for project definition, compiler settings, etc.
• Files required for deployment.

A project (like most Java projects) is an Eclipse-based project designed to be hosted on Tomcat.

Now give the above information, I decided to document the entire project in three different documents

• A document explaining the source code, etc.
• A document explaining the purpose of files and directories required for compiler options, project definitions, etc.
• A document that explains the structure of the deployment directory.

Or, alternatively, I could create a single document with three sections, which explain 1-3 above.

Now questions

• Is this the right approach?
• Are there any other methodologies that I can implement or borrow?
• Are there any other suggestions, etc. that you can add to this approach.

Any further information would be helpful.

Thanks for the ton in advance