Here is a list of all files with brief descriptions:

agent.cc
agent.h
agent_managed.h
any.hpp
bid.h
bid_portfolio.cc
bid_portfolio.h
blob.h
builder.h
building_manager.cc
building_manager.h
capacity_constraint.h
coin_helpers.cc
coin_helpers.h
commodity.cc
commodity.h
commodity_producer.cc
commodity_producer.h
commodity_producer_manager.cc
commodity_producer_manager.h
commodity_recipe_context.cc
commodity_recipe_context.h
comp_math.cc
comp_math.h
composition.cc
composition.h
context.cc
context.h
cram.c
cram.h
cram.hpp
cyc_arithmetic.cc	Implements the CycArithmetic class for various arithmetic algorithms
cyc_arithmetic.h	Declares the CycArithmetic class, which holds arithmetic algorithms
cyc_limits.h
cyc_std.h
cyclus.h
datum.cc
datum.h
db_init.cc
db_init.h
decay.cpp
decay.h
decayer.cc
decayer.h
discovery.cc
discovery.h
dynamic_module.cc
dynamic_module.h
enrichment.cc
enrichment.h	Top-level enrichment functionality
env.cc
env.h
error.cc
error.h
eventhooks.cc
eventhooks.cc.h
eventhooks.h
exchange_context.h
exchange_graph.cc
exchange_graph.h
exchange_manager.h
exchange_solver.cc
exchange_solver.h
exchange_translation_context.h
exchange_translator.h
facility.cc
facility.h
greedy_preconditioner.cc
greedy_preconditioner.h
greedy_solver.cc
greedy_solver.h
hdf5_back.cc
hdf5_back.h
hdf5_back_gen.py
infile_converters.cc
infile_converters.h
infile_tree.cc
infile_tree.h
institution.cc
institution.h
intrusive_base.h
l_matrix.cc
l_matrix.h
logger.cc
logger.h	Code providing rudimentary logging capability for the Cyclus core
mat_query.cc
mat_query.h
material.cc
material.h
matl_buy_policy.cc
matl_buy_policy.h
matl_sell_policy.cc
matl_sell_policy.h
mock_sim.cc
mock_sim.h
OsiCbcSolverInterface.cpp
OsiCbcSolverInterface.hpp
OsiCbcSolverInterface_2_5.cpp
OsiCbcSolverInterface_2_5.hpp
OsiCbcSolverInterface_2_8.cpp
OsiCbcSolverInterface_2_8.hpp
OsiCbcSolverInterface_2_9.cpp
OsiCbcSolverInterface_2_9.hpp
platform.h
position.cc
position.h
prettyprint.hpp
product.cc
product.h
prog_solver.cc
prog_solver.h
prog_translator.cc
prog_translator.h
pyhooks.cc
pyhooks.h
pyinfile.cc
pyinfile.cc.h
pyinfile.h
pymodule.cc
pymodule.cc.h
pymodule.h
pyne.cc
pyne.h
query_backend.h
rec_backend.h
recorder.cc
recorder.h
region.cc
region.h
relax_ng_validator.cc
relax_ng_validator.h
request.h
request_portfolio.h
res_buf.h
res_manip.cc
res_manip.h
res_map.h
res_tracker.cc
res_tracker.h
resource.cc
resource.h
resource_buff.cc
resource_buff.h
resource_exchange.h
sim_init.cc
sim_init.h
solver_factory.cc
solver_factory.h
sqlite_back.cc
sqlite_back.h
sqlite_db.cc
sqlite_db.h
state_wrangler.h
supply_demand_manager.cc
supply_demand_manager.h
symbolic_function_factories.cc
symbolic_function_factories.h
symbolic_functions.cc
symbolic_functions.h
time_listener.h
timer.cc
timer.h
timeseries.cc
timeseries.h
trade.h
trade_executor.h
trader.h
trader_management.h
uniform_taylor.cc
uniform_taylor.h
unix_helper_functions.h
use_matrix_lib.h
version.cc
version.h
windows_helper_functions.h
xml_file_loader.cc
xml_file_loader.h
xml_flat_loader.cc
xml_flat_loader.h
xml_parser.cc
xml_parser.h