Updated code architecture

Specifications/Code Architecture.md

 # Codebase Organization
 
-## Option One
-
-Each component in its own Git repository, completely independent of others.  In this case, interaction must be through JSON API calls between components.
-
-## Option Two
-
-Consider the following PHP namespace organization, with mirroring directory structure.
+We define the following PHP namespace organization, with mirroring directory structure.
 
 ```
 \snac
     \client
         \webui
-            index.php
             \workflow
         \rest
-            index.php
         \testui
     \server
-        index.php
         \workflow
         \identityReconciliation
         \dateParser
@@ -29,30 +20,21 @@ Consider the following PHP namespace organization, with mirroring directory stru
         \authorization
         \database                   % Database interaction (mainly wrappers)
         % possible wrappers for Neo4J and Elastic Search
+    \exceptions                     % SNAC exceptions to be thrown on error
+    \interfaces                     % interfaces used throughout the codebase
 ```
 
-In this organization, the codebase will be kept together.  The `index.php` markers are simply for readability.  Each of those files will be set up as main script for a service that the server will provide.  For example:
-
-```
-\snac\client\webui\index.php    at http://www.snaccooperative.org/
-                                serving HTML, JavaScript, and JSON
-\snac\client\rest\index.php     at http://api.snaccooperative.org/
-                                serving JSON, file downloads
-\snac\server\index.php          at http://localhost:xxxx/
-                                serving JSON and internal server data
-```
-
-A key note here is that the client applications (web ui and rest api) will then need to make internal server API calls over the local server API to handle any back-end requests.  This addresses a separation of concerns and keeps the server more secure.
 
-### Alternative 1 (Preferred)
+A key note here is that the client applications (web ui and rest api) will then need to make internal server API calls over the local server API to handle any back-end requests.  This addresses a separation of concerns, keeps the server more secure, and allows for a higher level of scalability.
 
-We may use the architecture above, but without the index.php files in respective namespaces.  In this case, all endpoints will share the same codebase, but with an index.php that includes the codebase and instantiates and executes the appropriate class.  Then, we may have:
+All endpoints (server, webui, and rest) will share the same codebase, but with an `index.php` that includes the codebase and instantiates and executes the appropriate handler class.  Then, we may have:
 
 ```
-/var/www/html       instantiates \snac\client\webui\WebUI
-/var/www/api        instantiates \snac\client\rest\RestAPI
-/var/www/internal   instantiates \snac\server\Server
+/var/www/snac-www        instantiates \snac\client\webui\WebUI
+/var/www/snac-api        instantiates \snac\client\rest\RestAPI
+/var/www/snac-internal   instantiates \snac\server\Server
 ```
+
 ### Repo Organization
 
 ```
@@ -60,9 +42,9 @@ We may use the architecture above, but without the index.php files in respective
     /src                % containing all snac sourcecode
         /snac           % ...
         /virtualhosts
-            /web
-            /rest
-            /server
+            /www        % landing for /var/www/snac-www
+            /rest       % landing for /var/www/snac-api
+            /internal   % landing for /var/www/snac-internal
     /test               % containing all unit tests (mirrors /src)
         /snac           % ...
     LICENSE             % code license