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Updated Installation (markdown)
File upload sizes and mysql max_allowed_packet
Adding link to NCBI-update README (coming next)
Update MySQL configs for UTF-8
Update php version requirement
Adding instructions for site-wide embargo via .htaccess
Adding a step to force all admin pages into HTTPS
Setting UTF-8 encoding and new instructions to 'config.php'.
Updating information on recursive MySQL procedures.
Standardizing on (and explaining) the example /path/to/local
Identifying likely locations for config files.
Enable short_open_tags in php
Let's try again, with terse instructions for a more experienced sysadmin.