did you apply to be in beta invite and submit domains for whitelisting https://community.letsencrypt.org/t/beta-program-announcements/1631/72 ?
Shure. This is command string:
./letsencrypt-auto --agree-dev-preview -d SERVERNAME.org --server https://acme-v01.api.letsencrypt.org/directory -a manual auth -v --debug
Just did I tried to do next sequence from this way Using the webroot domain verification method
- I did removed all configuration from local folder, /etc/letsencrypt/, /var/lib/letsencrypt/.
- I did reinstalled letsencrypt into /usr/local
- I did started /usr/local/letsencrypt/bootstrap/ubuntu
- I did checked activation of modules "headers" but did not found "letsencrypt": /user/lib/apache2/modules/mod_letsencrypt are not exists.
This variant is not to live.