no files in challenges other than i test one
a browse to http://foo.u/.well-known/acme-challenge/foo
does display the content of the file foo
<VirtualHost _default_:80>
ServerName foo.u
DocumentRoot "/home/acme/challenges"
<Directory "/home/acme/challenges">
AllowOverride FileInfo AuthConfig Limit Indexes
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Require all granted
Allow from all
</Directory>
Alias /.well-known/acme-challenge "/home/acme/challenges"
</VirtualHost>
i believe the problem is indeed perms for write, as the log message is
[Sun Dec 06 14:01:06.684373 2015] [core:error] [pid 759] (13)Permission denied: [client 42.28.0.666:35964] AH00132: file permissions deny server access: /home/acme/challenges/zeiHTeaxu_Uk-QT6-OTcjB6G6p3V_X5DGGh-EtNe11I
but i suspect the apache config more than file perms/owners, but acme user can write to a file in challenges, and a web browser can read that file. so i feel more stupid than usual.