Fix minor formatting errors in server documentation.

docs/source/server.rst

@@ -25,40 +25,41 @@ firewall, are beyond the scope of this documentation.
 
 The RPC service was created using `Apache Thrift`_.
 
-_`Apache Thrift`: https://thrift.apache.org/
+.. _`Apache Thrift`: https://thrift.apache.org/
 
 Starting the server
 -------------------
 
-There are two ways to start the server: via a Beanshell script and via
-the ImageJ GUI.
+There are three ways to start the server: via the command line, inside
+the ImageJ GUI, and via a Beanshell script.
 
-Beanshell script
-++++++++++++++++
+Command line
+++++++++++++
 
-There is an example script called **example_server.bsh** in the
-`scripts`_ folder of SASS that demonstrates how to launch the server
-through a Beanshell script. After creating a Microscope instance named
-*microscope*, simply create and launch the server with these lines ::
+Enter the following command in a console window to start the server
+from the command line ::
 
-  RPCServer server = new RPCServer(microscope, 9090);
-  server.serve();
+  java -jar PATH_TO_SASS_JAR -r CONFIGURATION_FILE
 
-Note that you will need to first import RPCServer with the command ::
+The above command requires two arguments. **PATH_TO_SASS_JAR** is the
+path and name of the SASS .jar file, which can be downloaded from the
+`releases`_ page of the GitHub repository. **CONFIGURATION_FILE** is a
+file that specifies the simulation configuration. This file can be
+created created and saved from inside the SASS ImageJ GUI.
 
-  import ch.epfl.leb.sass.server.RPCServer;
+The command will start the server on the default port, which was 9090
+at the time of this writing. If instead you wish to specify the port
+number, use ::
 
-This code will initialize the server to listen on port 9090 and launch
-it. If you run the script from the command line, then you can kill the
-server by typing **Ctrl-C**.
+  java -jar PATH_TO_SASS_JAR -p PORT -r CONFIGURATION_FILE
 
-_`scripts`: https://github.com/kmdouglass/SASS/tree/master/scripts
+.. _`releases`: https://github.com/LEB-EPFL/SASS/releases
 
 ImageJ
 ++++++
 
 1. Open the server configuration dialog from the menu bar by clicking
-**Plugins > SASS > Server**.
+   **Plugins > SASS > Server**.
 2. Enter the port number you wish to use for communications with the
    server. Usually the default (9090) is fine.
 3. Next, you will need a configuration file that defines your
@@ -79,6 +80,27 @@ ImageJ
 If you are using Fiji, then you can see status updates from the server
 by navigating to **Window >> Console** on the menu bar.
 
+Beanshell script
+++++++++++++++++
+
+There is an example script called **example_server.bsh** in the
+`scripts`_ folder of SASS that demonstrates how to launch the server
+through a Beanshell script. After creating a Microscope instance named
+*microscope*, simply create and launch the server with these lines ::
+
+  RPCServer server = new RPCServer(microscope, 9090);
+  server.serve();
+
+Note that you will need to first import RPCServer with the command ::
+
+  import ch.epfl.leb.sass.server.RPCServer;
+
+This code will initialize the server to listen on port 9090 and launch
+it. If you run the script from the command line, then you can kill the
+server by typing **Ctrl-C**.
+
+.. _`scripts`: https://github.com/kmdouglass/SASS/tree/master/scripts
+
 Server communications
 ---------------------
 
@@ -164,7 +186,9 @@ rudimentary Python client to control a SASS simulation.
 4. Install the Thrift bindings for Python, preferably inside a virtual
    environment. `pip install thrift`
 4. Enter the folder **gen-py** (or move it to a convenient directory).
-5. Create a file named client.py and add the following code ::
+5. Create an emtpy file named client.py.
+
+Inside the client.py file, you will need to add the following code ::
 
   from thrift import Thrift
   from thrift.transport import TSocket
@@ -207,7 +231,7 @@ tif-encoded byte strings.** You therefore will need the libtiff
 library in your target language to decode them. In Python, this can be
 provided by `pillow`_.
 
-_`Apache Thrift`: https://thrift.apache.org/
-_`Get Apache Thrift`: https://thrift.apache.org/download
-_`RPCServer.thrift`: https://github.com/LEB-EPFL/SASS/blob/master/thrift/RPCServer.thrift
-_`pillow`: https://github.com/python-pillow/Pillow
+.. _`Apache Thrift`: https://thrift.apache.org/
+.. _`Get Apache Thrift`: https://thrift.apache.org/download
+.. _`RPCServer.thrift`: https://github.com/LEB-EPFL/SASS/blob/master/thrift/RPCServer.thrift
+.. _`pillow`: https://github.com/python-pillow/Pillow