definitions.js JavaScript page which is created by PHP, which defines useful URLs, etc. Then knowledge only needs to be embedded in the database, and maybe some PHP scripts (eg server_config.php).
tmpwatch can be used safely.
atime enabled.
apache configuration script sets appropriate headers so that images are cached for a reasonable amount of time to reduce load on the web server.
mod_asis; if the images are prepended with HTTP headers they can be sent 'as is', which may provide a reduced latency, or increased delay when untarring.
project_pi table, with columns project_id, and contact_id. This allows mutliple PIs for each project. Create a similar tables project_contacts and project_institutes. Remove the pi_id and contact[1-4]_id columns from the programs table. Rename programs table to projects to follow THEMIS notation and avoid confusion with the term computer program.