Cleaning up the Markdown a bit

I saw that some sections had wrong section numbers as they were hardcoded instead of making use of Markdown's auto-numbering.
I repaired the indents for auto-numbering to work in the first half of the document and didn't touch the 2nd half where things looked okay.

README.md

@@ -41,18 +41,19 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
 ### ISIS Installation With Conda
 
 1. Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: [Anaconda installer](https://www.anaconda.com/download), [Miniconda installer](https://conda.io/miniconda.html)
-2.  If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment.
+1. If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment.
     
+    ```bash
     chmod +x Anaconda3-5.3.0-Linux-x86_64.sh
     ./Anaconda3-5.3.0-Linux-x86_64.sh
-
-
+    ```
     This will start the Anaconda installer which will guide you through the installation process.
 
-3.  If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86\_64.pkg) will be downloaded. Double-click on the file to start the installation process.
-4.  After the installation has finished, open up a bash prompt in your terminal window.
-5.  Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands:
+1. If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86\_64.pkg) will be downloaded. Double-click on the file to start the installation process.
+1. After the installation has finished, open up a bash prompt in your terminal window.
+1. Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands:
 
+    ```bash
     #Create a new conda environment to install ISIS in
     conda create -n isis python=3.6
 
@@ -82,22 +83,27 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
     #The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:
 
     conda config --env --add channels usgs-astrogeology
+    ```
     
-6.  Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver:
+1. Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver:
     
+    ```bash
     conda install -n base -c conda-forge mamba
+    ```
+1. The environment is now ready to download ISIS and its dependencies:
 
-7.  The environment is now ready to download ISIS and its dependencies:
-
+    ```bash
     mamba install -c usgs-astrogeology isis
+    ```
     
     If you would like to work with our latest ISIS version 3, rather than updating
     to ISIS 4, instead run:
 
+    ```bash
     mamba install -c usgs-astrogeology isis=3.10.0
+    ```
 
-
-8.  Finally, setup the environment variables:
+1. Finally, setup the environment variables:
 
     ISIS requires several environment variables to be set in order to run correctly.
     The variables include: ISISROOT and ISISDATA.
@@ -109,7 +115,7 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
 
     There are two methods to configure the environment variables for ISIS:
 
-    7.1 Using `conda env config vars` *preferred*
+    1. Using `conda env config vars` *preferred*
 
        Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8.
        This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed.
@@ -142,7 +148,7 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
        **Note** This method will not enable tab completion for arguments in C-Shell.
 
 
-    7.2 Using the provided isisVarInit.py script:
+    1. Using the provided isisVarInit.py script:
 
        To use the default values for: `$ISISROOT` and `$ISISDATA`, run the ISIS variable initialization script with default arguments:
 
@@ -159,7 +165,6 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
            prior to Anaconda 3.4 - source activate isis
 
 
-
 ### Installation with Docker
 The ISIS production Dockerfile automates the conda installation process above.
 You can either build the Dockerfile yourself or use the