Who know, how to rename template directory? From /themes/site_themes/agile_records To /themes/site_themes/custom_name
it is not really template directory - it is folder for template presets which use during install. After installation only images/js use from this folder. To change it you will need to make search agile_records and replace it with custom_name in DB or in files (before install).
Folder for saving template files, you can setup in
CP Home -> Design -> Template Manager -> Global Template Preferences