server {
    listen 443 ssl;
    # listen [::]:443 ssl;

    server_name machine.example;

    root /srv/www/default;

    location /ports {
        alias /var/ports/ports;
        autoindex on;
    }

    location /distfiles {
        alias /var/ports/distfiles;
        autoindex on;
    }

    location /packages {
        root /var/ports/packages;
        autoindex off;
    }


    location /bug {
        index index.php;
    	alias /srv/www/default/flyspray;
        try_files $uri $uri/ index.php$is_args$args;
    }

    location ~  ^/bug(.+\.php)$ { ### This location block was the solution
    	alias /srv/www/default/flyspray;

	fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_index index.php;
        try_files $uri /index.php =404;	
        include /etc/nginx/fastcgi_params;
        fastcgi_param SCRIPT_FILENAME $document_root$1;
        # fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_pass 127.0.0.1:9000;
    }

    location / {
    	alias /srv/www/default/pmwiki/;
	index pmwiki.php
        try_files $uri $uri/ /pmwiki.php$is_args$args;
    }

    location ~ \.php$ {
    	alias /srv/www/default/pmwiki;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_index pmwiki.php;
        try_files $uri /pmwiki.php =404;
        include /etc/nginx/fastcgi_params;
        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
        # fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_pass 127.0.0.1:9000;
    }
}