The final project documentation includes:

Final report
Comments embedded in the code

Here's a generic outline for the final report (page estimates are approximate):

Introduction (3-4 pages)
talk about the motivations for, and objectives of, the project
include a background section that introduces your application domain
include a section that discusses similar projects and how they differ from this project
explain the technical challenges for the project

Functional and Nonfunctional Requirements (8-12 pages)
this would be a much shortened counterpart to what you did in CSCI 4830
you can follow the outline for the requirements specification document in CSCI 4830
be sure to include use cases for the main services you will support
other models can also be used if appropriate for your project domain

Architecture and Design (8-12 pages)
this is also a much shortened counterpart to what you did in CSCI 4830
you can follow the outline for the design document in CSCI 4830
the following should be described and modeled: architecture, modules and their interfaces, database (if applicable) - we may have to iterate to get the desired details
in the textual description, talk about the rationales for various design decisions and identify which code modules or components were reused (e.g., open source libraries, existing code from another project, etc.)
some screenshots

Implementation Issues - various issues that cropped up in the process of writing the code (1-2 pages)

Testing (2-3 pages)
discuss the overall testing strategy followed
list the tests conducted

Lessons Learned (3-5 pages)
[individual] what you learned in this project; for example:
how had the project helped improve your understanding of CS-related principles, concepts or theories?
how had your CS background helped with this project?
[individual or team] if you had the chance to do it over, what would you do differently
[team] based on your experience, suggest some future extensions

Appendix
Team weekly meeting notes
Individual journals of weekly activities

As for the embedded code comments, format them in a way that can be processed by a document generation tool (like Doxygen).