Here is a list of all files with brief descriptions:

addflags.f
advanc.f
allowflag.f
amr2.f90
amr_module.f90
auxcoarsen.f
b4step2.f90
baseCheck.f
basic.f
bc2amr.f
birect.f
bound.f90
bound_orig.f90
bufnst2.f
cellave.f
check.f
check4nans.f90
check_hdf.f
cleanup.f
coarseGridFlagSet.f
coarsen.f
colate2.f
conck.f
copysol.f
cstore.f
domain.f
domcopy.f
domgrid.f
domprep.f
domshrink.f
domup.f
drivesort.f
errest.f
errf1.f
estdt.f
fdisc.f
filpatch.f90
filpatch_orig.f90
filval.f90
filval_orig.f90
findcut.f
fixcapaq.f
flag2refine2.f90
flagcheck.f
flagger.f
flagregions.f90
flagregions2.f90
flglvl2.f
flux2.f
flux2_dimSplit.f
fluxad.f
fluxsv.f
fss.f
gauges_module.f90
gfixup.f
ginit.f
grdfit2.f
griddomcopy.f
griddomshrink.f
griddomup.f
icall.f
igetsp.f
init_alloc.f90
init_iflags.f
inlinelimiter.f
intcopy.f
intfil.f90
limiter.f
moment.f
nestck2.f
nodget.f
opendatafile.f
outmsh.f
outtre.f
outval.f
outvar.f
philim.f
physbd.f
prefilp.f90
prefilp_orig.f90
preicall.f
preintcopy.f
prepbigstep.f
prepc.f
prepf.f
prepregstep.f
projec2.f
putnod.f
putsp.f
qad.f
qinit.f90
quick_sort1.f
reclam.f
regions_module.f90
regrid.f
resize_alloc.f90
resize_alloc_static.f90
restrt.f
restrt_alloc.f90
restrt_hdf.f
rpn2from1d.f
saveqc.f
setaux.f90
setdomflags.f
setflags.f
setgauges.f
setgrd.f
setIndices.f
setPhysBndry.f
setPhysBndryFlags.f
setprob.f90
setuse.f
shiftset2.f
signs.f
smartbis.f
spest2.f
src1d.f90
src2.f90
step2.f90
step2_sweep.f90
step2x.f90
step2y.f90
stepgrid.f
stepgrid_dimSplit.f
stst1.f
tick.f
trimbd.f90
upbnd.f
update.f
valout.f
zeroin.f