HOOMD-blue top-level directory structure:
 /CMake     - helper cmake scripts, common to main hoomd and plugin builds 
 /data      - Storage location for art, scripts, et cetera. that are needed for development but do not need to be installed or
              used in the build process.
 /doc       - Documentation source (compiled into easily readable documentation by doxygen during the build process)
 /installer - Scripts and settings for the installer
 /libhoomd  - C++ source code for the main hoomd library
 /python-module   - High level API code for using hoomd within python scripts
 /python-runner   - Runner script to execute python in the proper environment to load modules in python-module
 /microbenchmarks - A sandbox for playing with new computation techniques on the GPU
 /share     - Contains scripts, templates, and other files that are installed in the OS share directory
 /test      - All manner of tests to verify that a hoomd build is running correctly

For full documentation on hoomd, build it from source or point your web browser to
http://codeblue.umich.edu/hoomd-blue/doc-trunk/