Hi Luigi,

I have something to add to only one of your points:

On Sat, Dec 1, 2012 at 8:22 PM, luigi scarso <luigi.scarso@gmail.com> wrote:
On Sat, Dec 1, 2012 at 5:22 PM, Steve White <stevan.white@gmail.com> wrote:
>
> 3) The command
>       mtxrun --script font --reload
>     searches a bunch of directories for fonts, but not the directory
>       texmf-project/fonts/
>     My work-around was just to copy the *.ttf files to
>       texmf-fonts/
>     and then re-do the mtxrun line.
Hm, no, this is strange --- are you sure ?
If I remove the files from texmf-project/fonts/
and make
mtxrun --script font --reload
I have
mtxrun --script font --list --all|grep Free
But when I copy them again in
texmf-project/fonts/
and
mtxrun --script font --reload
then
mtxrun --script font --list --all|grep Free
then I see

freemono                             freemono
FreeMono.ttf
freemonobold                         freemonobold
FreeMonoBold.ttf
freemonoboldoblique                  freemonoboldoblique
FreeMonoBoldOblique.ttf
freemononormal                       freemonooblique
FreeMonoOblique.ttf
freemonooblique                      freemonooblique
FreeMonoOblique.ttf
freesans                             freesans
FreeSans.ttf
freesansbold                         freesansbold
FreeSansBold.ttf
freesansboldoblique                  freesansboldoblique
FreeSansBoldOblique.ttf
freesansdemi                         freesansbold
FreeSansBold.ttf
freesansnormal                       freesansoblique
FreeSansOblique.ttf
freesansoblique                      freesansoblique
FreeSansOblique.ttf
freeserif                            freeserif
FreeSerif.ttf
freeserifbold                        freeserifbold
FreeSerifBold.ttf
freeserifbolditalic                  freeserifbolditalic
FreeSerifBoldItalic.ttf
freeserifitalic                      freeserifitalic
FreeSerifItalic.ttf
freeserifnormal                      freeserifitalic
FreeSerifItalic.ttf

I also see

fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for otf files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for OTF files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for ttf files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for TTF files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for ttc files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for TTC files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for dfont files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for DFONT files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for afm files
fonts           | names | scanning
/opt/luatex/standalone-mkiv/tex/texmf-project for AFM files

The problem with texmf-fonts/
is that is keep in sync with the original source, and hence the files
can be deleted.


I can assure you, this fonts/ directory was not in the list produced by the mtxrun command on my system.

Something is different between your system and mine.
This might be worth investigating.  (But I won't have time for it!)

Perhaps you have a file somewhere that adds this other directory.  This is my best guess.

It is also possible something was left over on my system from the previous distro installation.  However I removed that installation with the dpkg --purge command, which should have removed all settings files.  I didn't alter any configuration files myself, I only tried (unsuccessfully) to run context on some tex files.

As I had only turned context on a few times, and never done any configuration, it is easy to reproduce my setup:  Start with the latest Ubuntu, and install the 'context' package. 
Then remove it with --purge, and follow your instructions to install the recent 'context' in /opt.

Cheers!