Initial attempt at revamping project make file. Still needs work
Git-ignore directives for OS-specific files and IDE-specific files should go in the environment's global .gitignore file.  See http://stackoverflow.com/questions/1753070/git-ignore-files-only-locally
Ignore files/ directory and settings.php.
Version control default.settings.php to make it easier to notice Drupal core updates that affect settings.php.
Move the Nesi Bootstrap subtheme into it's own directory.
Remove bootstrap contrib theme and third party libraries from repository since they should be managed in make file.
Drupal core update to default.settings.php.
Move custom/ directory wrapping custom modules.
Removed outdated and misleading README files.
Add Drush aliases file.
Working on the make file to get it working.
Renaming the drush-make file to be more concise but clearer.
Updates to drush aliases file and sql-sync configuration.
Handle drush alias-inheritance with drush alias 'parent' instead of PHP array merging.
local.settings.php added for Aegir environment
Document the new process for site development, environment configuration, deploys, environment updates.
Some additional documentation tweaks.
Simplify make file.
Add Boostrap correctly.
Clean up documentation of the make file.