Updated ignore directories and files

Added per-instance base main-ext.php file to gitignore.
Runtime files should also not be included in git commits.
Removed per-instance configuration
Installation independent of previous install

Before this update, you needed to include a ".install" file in a
specific directory to invoke the installer. Now the application will
look for a specific file generated by an installer
(protected/config/main-ext.php) which has the database connection
details. If this file does not exist (cannot connect to DB) then it will
invoke the installer automatically.

To reinstall the application, you will need to delete the main-ext.php
file from the configuration directory.
Updated UI changes for Flashes

Flashes for "warnings" now aren't so ugly. They are yellow and have a
flag icon. Also updated Jquery UI buttons so they are properly padded.