Same problem, fresh rsync from minimals:

C:\Users\chesky\Programs\ConTeXt>luatools --ini --compile cont-en

LuaTools | creating initialization file cont-en
LuaTools | using library path :
C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base
LuaTools | using lua libraries: l-string.lua l-lpeg.lua l-table.lua
l-boolean.lua l-number.lua l-set.lua l-unicode.lua l-md5.lua l-os.lua
l-io.lua l-file.lua l-url.lua l-dir.lua l-utils.lua l-tex.lua
luat-env.lua luat-lib.lua luat-inp.lua luat-tmp.lua luat-zip.lua
luat-tex.lua
LuaTools | using compiled initialization file cont-en.luc
LuaTools | using lua initialization file cont-en.luc
LuaTools | running command: luatex --ini --lua="cont-en.luc"
"C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/cont-en.tex"
\dump
(C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/cont-en.tex
(C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/context.tex
(C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/syst-pln.tex)
(C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/syst-prm.tex)
(C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/luat-env.tex)
(C:/Users/chesky/Programs/ConTeXt/texmf-context/tex/context/base/luat-lib.tex
! LuaTeX error ...ams/ConTeXt/texmf-context/tex/context/base/l-aux.lua:55:
attempt to call field 'Carg' (a nil value).
\ctxluabytecode ...ode " .. "#1" .. str) end end }

\registerctxluafile ...{\the \luabytecodecounter }
                                                  \fi
l.45 \registerctxluafile{l-aux}    {1.001}

?

Multiple runs of luatools --selfupdate and luatools --generate don't help.

I'll try pulling again later, see if that works.

--Joel
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