I apologize in advance if this question is too general - I'm happy to share 
specifics as needed. I'll attach a couple key files as a start on that.

I used the online tool PuPHPet to create a CentOS box that was close to 
meeting my needs, but because of that, my Puppet files are apparently more 
complex than they need to be (all examples I have seen in tutorials are far 
simpler). Then, because I was completely new to all this, I made changes to 
my actual server (by SSHing into my VM and rummaging around) while having 
absolutely no idea how to reflect those changes in the Puppet files.

Since then I have procrastinated on climbing this learning curve, but 
recently I upgraded Vagrant on the host, and now "vagrant global-status" 
says, "There are no active Vagrant environments on this computer! Or, you 
haven't destroyed and recreated Vagrant environments that were started with 
an older version of Vagrant." Hmph! I know I will lose my changes if I 
destroy and recreate, so I really need to figure out how to clean up my 
Puppet files. 

The directory structure looks like this:

│  Vagrantfile
│  
├─.vagrant
│  └─machines
│      └─default
│          └─virtualbox
│                  action_provision
│                  action_set_name
│                  id
│                  private_key
│                  synced_folders
│                  
└─puphpet
    │  config.yaml
    │  
    ├─files
    │  ├─dot
    │  │      .bash_aliases
    │  │      .vimrc
    │  │      
    │  ├─exec-always
    │  │      empty
    │  │      
    │  └─exec-once
    │          empty
    │          
    ├─puppet
    │      hiera.yaml
    │      manifest.pp
    │      Puppetfile
    │      
    └─shell
            execute-files.sh
            initial-setup.sh
            install_phalcon-devtools.sh
            install_phalcon.sh
            librarian-puppet-vagrant.sh
            os-detect.sh
            self-promotion.txt
            update-puppet.sh

puphpet/puppet/manifest.pp alone is 920 lines! I'm pretty sure most of 
that, as well as many of the other files, is unneeded code (I keep seeing 
things like "if $::osfamily == 'debian'...", for example). But the syntax 
is new to me, so I'm afraid to start slashing chunks of it.

A key piece of work I remember doing was on the nginx configuration, so 
I'll throw it out as a concrete example. A tree of the VM's /etc/nginx/ is 
as follows, with sizes and dates (as you can probably guess, I made the box 
in February last year and then fiddled with it off and on over the next 
couple months):

├── [       4096 Mar  6  2014]  conf.d
│   ├── [        888 Feb 13  2014]  default.conf
│   ├── [        427 Feb 11  2014]  example_ssl.conf
│   ├── [        415 Feb 13  2014]  proxy.conf
│   └── [       1469 Apr 26  2014]  vhost_autogen.conf
├── [       4096 Feb 13  2014]  conf.mail.d
├── [        963 Mar  6  2014]  fastcgi_params
├── [       4096 Mar  6  2014]  includes.d
│   └── [       1127 Mar 25  2014]  fastcgi_common
├── [       2837 Feb 11  2014]  koi-utf
├── [       2223 Feb 11  2014]  koi-win
├── [       3463 Feb 11  2014]  mime.types
├── [        565 Apr 19  2014]  nginx.conf
├── [        596 Feb 11  2014]  scgi_params
├── [        623 Feb 11  2014]  uwsgi_params
└── [       3610 Feb 11  2014]  win-utf

Most of the work I remember doing is in vhost_autogen.conf, but the string 
"autogen" doesn't appear in manifest.pp, so I don't know what code created 
that file. Perhaps I'm hopelessly ignorant, but can someone point me in the 
right direction? It's too bad that it isn't possible to create a Puppet 
manifest from an existing server... ;-)

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Attachment: manifest.pp
Description: Binary data

server {
  listen 80;
  server_name *.kizunadb.dev;
  root /var/www/kizunadb/public;

  access_log  /var/log/nginx/kizunadb.access.log;
  error_log   /var/log/nginx/kizunadb.error.log;
  
  index index.php index.html index.htm;

  try_files $uri $uri/ @rewrite;

  location @rewrite {
    rewrite ^/(.*)$ /index.php?_url=/$1;
  }
  location ~ ^(.+\.php)(/.*)?$ {
    fastcgi_param PATH_INFO $fastcgi_path_info;
    fastcgi_param PATH_TRANSLATED $document_root$fastcgi_path_info;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;

    fastcgi_pass unix:/var/run/php5-fpm.sock;
    fastcgi_split_path_info ^(.+\.php)(/.+)$;
    include fastcgi_params;
  }
}

server {
  listen 80 default_server;
  server_name     l4jp.dev;
  access_log /var/log/nginx/l4jp.dev.access.log;
  error_log /var/log/nginx/l4jp.dev.error.log;

  location / {
    root  /var/www/l4jp/public;
    try_files  $uri  $uri/  /index.php?$args ;
    index  index.html index.htm index.php;
  }

  location ~ \.php$ {
    root  /var/www/l4jp/public;
    try_files  $uri  $uri/  /index.php?$args ;
    index  index.html index.htm index.php;
    fastcgi_index index.php;
    fastcgi_param PATH_INFO $fastcgi_path_info;
    fastcgi_param PATH_TRANSLATED $document_root$fastcgi_path_info;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;

    fastcgi_pass unix:/var/run/php5-fpm.sock;
    fastcgi_split_path_info ^(.+\.php)(/.+)$;
    include fastcgi_params;
  }

}

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