Here is a list of all files with brief descriptions:

include/clumps.h [code]	Clump functions: concentration, spatial and mass distribution, ...
include/geometry.h [code]	Geometric transformation from spher.Gal.coord. to Cartesian Gal.coord. (and vice-versa)
include/inlines.h [code]	Inline variables/macros (constants, conversions)
include/integr.h [code]	Integration routines (adaptive refinement for lin. and log. step)
include/integr_los.h [code]	Integrates along a l.o.s. (line of sight) any function $f(l,\Omega)$ : $\;\; I_{l.o.s} \equiv \int_{\Delta\Omega}\int_{l_{min}}^{l_{max}} f (l,\Omega) \,dld\Omega \,\,\;\;$
include/janalysis.h [code]	-factor (Gal. w/o sub-halo mean/drawn w/o list) for annihil. $[M_\odot^2\,\,kpc^{-5}]$ or decay $[M_\odot\,\, kpc^{-2}]$
include/misc.h [code]	Miscellaneous simple functions used in several places
include/params.h [code]	Global parameters declaration/initialisation (Galaxy, DM, Cosmology, SIMU)
include/profiles.h [code]	Profile $\rho(r)$ $[M_\odot\,\,kpc^{-3}]$ and related functions (applicable for halos, sub-halos...)
include/spectra.h [code]	Spectra from DM annihilations: $\Phi^{PP}(E_{\gamma})\equiv \frac{d\Phi_{\gamma}}{dE_{\gamma}} \equiv \frac{1}{4\pi}\frac{\langle\sigma_{ann}v\rangle}{2m_{\chi}^{2}} \cdot \sum_{f}\frac{dN^{f}_{\gamma}}{dE_{\gamma}}B_{f}$
include/stat.h [code]	Statistical functions: mean and variance of several quantities
src/clumps.cc [code]	(see clumps.h)
src/clumpy.cc [code]	CLUMPY executable (profiles, 1D or 2D- skymaps, stat. analysis, ...)
src/geometry.cc [code]	(see geometry.h)
src/integr.cc [code]	(see integr.h)
src/integr_los.cc [code]	(see integr_los.h)
src/janalysis.cc [code]	(see janalysis.h)
src/misc.cc [code]	(see misc.h)
src/params.cc [code]	(see params.h)
src/profiles.cc [code]	(see profiles.h)
src/spectra.cc [code]	(see spectra.h)
src/stat.cc [code]	(see stat.h)