Make formatting changes to directory structure page.

docs/design/directory-structure.md

@@ -27,6 +27,7 @@ Contains the [Common Infrastructure for Modeling the Earth (CIME)](https://githu
 ### **components/**
 
 Contains the following other CESM components:
+
 - [Community Data Models for Earth Prediction Systems (CDEPS)](https://github.com/ESCOMP/CDEPS)
 - [CICE sea ice model](https://github.com/ESCOMP/CESM_CICE)
 - [Community Ice Sheet Model (CISM)](https://github.com/ESCOMP/CISM-wrapper)
@@ -40,6 +41,7 @@ Contains the following other CESM components:
 ### **libraries/**
 
 Contains the following external libraries:
+
 - [Flexible Modeling System (FMS)](https://github.com/ESCOMP/FMS_interface.git)
 - [Parallel IO (PIO)](https://github.com/NCAR/ParallelIO)
 
@@ -55,10 +57,10 @@ These directories represent code and tools that is solely contained within the C
 
 Contains the SIMA-specific python and XML configuration routines used by CIME and the CCPP-framework to properly configure and build a CAM-SIMA simulation, including the CCPP-generated caps and namelist files.
 
-**Subdirectories/**:
+**Subdirectories**:
 
 - testdefs - Location of the CAM-SIMA regression test list and associated files used by CIME during regression (system) testing.
-   - testmods_dirs/cam - Location of CAM-SIMA case configuration files used during CIME regression testing.
+    - testmods_dirs/cam - Location of CAM-SIMA case configuration files used during CIME regression testing.
 
 ### **docker/**
 
@@ -76,7 +78,7 @@ Contains everything needed to perform software testing and validation of CAM-SIM
 
 - system/ - Includes scripts needed to run CIME (integration) regression tests.
 - unit/   - Includes scripts and source code needed to run CAM-SIMA unit tests.
-   - sample_files/ - Contains files that are used to validate the unit test results.
+    - sample_files/ - Contains files that are used to validate the unit test results.
 
 ### **tools/**
 
@@ -109,12 +111,12 @@ Contains all of the dynamical core (dycore) source code.
 **Subdirectories**:
 
 - mpas/ - Contains all of the source code needed for SIMA to properly couple to the [MPAS dynamical core](https://github.com/MPAS-Dev/MPAS-Model).
-   - dycore/ (external) - External submodule that contains the MPAS dycore code.
+    - dycore/ (external) - External submodule that contains the MPAS dycore code.
 - none/ - Contains the "null" dycore source code, which allows physics and chemistry routines to be forced with atmospheric data coming directly from input files as opposed to dycore calculations.
 - se/ - Contains all of the source code needed for SIMA to properly couple to the [Spectral Element dynamical core](https://ncar.github.io/CAM/doc/build/html/cam5_scientific_guide/dynamics.html#spectral-element-dynamical-core).
-   - dycore/ - Contains the internal SE dycore source code files.
+    - dycore/ - Contains the internal SE dycore source code files.
 - tests/ - Contains the source code needed to configure analytic initial conditions for dycores.
-   - initial_conditions/ - Contains source code needed to configure specific analytic initial conditions formulations.
+    - initial_conditions/ - Contains source code needed to configure specific analytic initial conditions formulations.
 - utils/ - Contains utility code used by all dycores in SIMA.
 
 ### **physics/**