You can use:
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
#rewrite project assets
RewriteCond %{REQUEST_URI} !/assets
RewriteRule (.*)/assets(.*) projects/$1/assets$2 [L]
#rewrite everything else
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$0 [PT,L,NC]