Magento 2 Nginx – Clean Install Cannot Access Admin, Index.php Added to URLs

I have successfully installed Magento 2 locally. I'm using nginx and I can access the home page just fine. But, all links have "/index.php" added to them, and when I click them I get shown a 404. So for example clicking on "create account" takes me to:

http://mysite.dev//index.php/customer/account/login/

… and shows me a 404. If I change it to:

/customer/account/login/

… the signup page displays correctly.

The biggest problem is that when I try to hit the admin, I get redirected to an index.php page that doesn't work if I update the URL.

So hitting this URL:

/admin/

Redirects to:

/index.php/admin/admin/index/index/key/9f5bcfba36a2cf8ac7ceaaddfa87ea47c41d621a428e400d74f9a94994785125/

… showing me a 404 again. Changing it to:

/admin/admin/index/index/key/9f5bcfba36a2cf8ac7ceaaddfa87ea47c41d621a428e400d74f9a94994785125/

… redirects me back to the index.php URL.

My nginx setup is:

upstream fastcgi_backend {
    server  127.0.0.1:9000;
}

server {
    listen 80;
    server_name mysite.dev;
    set $MAGE_ROOT /var/www/mysite.com;
    set $MAGE_MODE develop;
    include global/magento2.conf;
}

and global/magento2.conf is:

root $MAGE_ROOT/pub;

index index.php;
autoindex off;
charset UTF-8;
error_page 404 403 = /errors/404.php;
add_header "X-UA-Compatible" "IE=Edge";

# PHP entry point for setup application
location ~* ^/setup($|/) {
    root $MAGE_ROOT;
    location ~ ^/setup/index.php {
        fastcgi_pass   fastcgi_backend;
        fastcgi_index  index.php;
        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
        include        fastcgi_params;
    }

    location ~ ^/setup/(?!pub/). {
        deny all;
    }

    location ~ ^/setup/pub/ {
        add_header X-Frame-Options "SAMEORIGIN";
    }
}

# PHP entry point for update application
location ~* ^/update($|/) {
    root $MAGE_ROOT;

    location ~ ^/update/index.php {
        fastcgi_split_path_info ^(/update/index.php)(/.+)$;
        fastcgi_pass   fastcgi_backend;
        fastcgi_index  index.php;
        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
        fastcgi_param  PATH_INFO        $fastcgi_path_info;
        include        fastcgi_params;
    }

    # Deny everything but index.php
    location ~ ^/update/(?!pub/). {
        deny all;
    }

    location ~ ^/update/pub/ {
        add_header X-Frame-Options "SAMEORIGIN";
    }
}

location / {
    try_files $uri $uri/ /index.php?$args;
}

location /pub/ {
    location ~ ^/pub/media/(downloadable|customer|import|theme_customization/.*\.xml) {
        deny all;
    }
    alias $MAGE_ROOT/pub/;
    add_header X-Frame-Options "SAMEORIGIN";
}

location /static/ {
    # Uncomment the following line in production mode
    # expires max;

    # Remove signature of the static files that is used to overcome the browser cache
    location ~ ^/static/version {
        rewrite ^/static/(version\d*/)?(.*)$ /static/$2 last;
    }

    location ~* \.(ico|jpg|jpeg|png|gif|svg|js|css|swf|eot|ttf|otf|woff|woff2)$ {
        add_header Cache-Control "public";
        add_header X-Frame-Options "SAMEORIGIN";
        expires +1y;

        if (!-f $request_filename) {
            rewrite ^/static/(version\d*/)?(.*)$ /static.php?resource=$2 last;
        }
    }
    location ~* \.(zip|gz|gzip|bz2|csv|xml)$ {
        add_header Cache-Control "no-store";
        add_header X-Frame-Options "SAMEORIGIN";
        expires    off;

        if (!-f $request_filename) {
           rewrite ^/static/(version\d*/)?(.*)$ /static.php?resource=$2 last;
        }
    }
    if (!-f $request_filename) {
        rewrite ^/static/(version\d*/)?(.*)$ /static.php?resource=$2 last;
    }
    add_header X-Frame-Options "SAMEORIGIN";
}

location /media/ {
    try_files $uri $uri/ /get.php?$args;

    location ~ ^/media/theme_customization/.*\.xml {
        deny all;
    }

    location ~* \.(ico|jpg|jpeg|png|gif|svg|js|css|swf|eot|ttf|otf|woff|woff2)$ {
        add_header Cache-Control "public";
        add_header X-Frame-Options "SAMEORIGIN";
        expires +1y;
        try_files $uri $uri/ /get.php?$args;
    }
    location ~* \.(zip|gz|gzip|bz2|csv|xml)$ {
        add_header Cache-Control "no-store";
        add_header X-Frame-Options "SAMEORIGIN";
        expires    off;
        try_files $uri $uri/ /get.php?$args;
    }
    add_header X-Frame-Options "SAMEORIGIN";
}

location /media/customer/ {
    deny all;
}

location /media/downloadable/ {
    deny all;
}

location /media/import/ {
    deny all;
}

# PHP entry point for main application
location ~ (index|get|static|report|404|503)\.php$ {
    try_files $uri =404;
    fastcgi_pass   fastcgi_backend;
    fastcgi_buffers 1024 4k;

    fastcgi_param  PHP_FLAG  "session.auto_start=off \n suhosin.session.cryptua=off";
    fastcgi_param  PHP_VALUE "memory_limit=768M \n max_execution_time=600";
    fastcgi_read_timeout 600s;
    fastcgi_connect_timeout 600s;

    fastcgi_index  index.php;
    fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
    include        fastcgi_params;
}

gzip on;
gzip_disable "msie6";

gzip_comp_level 6;
gzip_min_length 1100;
gzip_buffers 16 8k;
gzip_proxied any;
gzip_types
    text/plain
    text/css
    text/js
    text/xml
    text/javascript
    application/javascript
    application/x-javascript
    application/json
    application/xml
    application/xml+rss
    image/svg+xml;
gzip_vary on;

# Banned locations (only reached if the earlier PHP entry point regexes don't match)
location ~* (\.php$|\.htaccess$|\.git) {
    deny all;
}