Bold directory headers in directory-structure section to improve read…

…ability.

docs/design/directory-structure.md

@@ -8,23 +8,23 @@ These directories contain external repository source code, libraries, or tools,
 
 Please note that any modifications to the source code in these directories should generally be made outside of CAM-SIMA and instead in the associated external repository listed below.
 
-### bin
+### **bin**
 
 Contains the `git-fleximmod` tool for downloading needed source code and software from external repositories.  More information on `git-fleximod` can be found [here](https://github.com/ESMCI/git-fleximod).
 
-### ccpp_framework
+### **ccpp_framework**
 
 Contains the core [CCPP-framework](https://github.com/NCAR/ccpp-framework) source code and tools.
 
-### ccs_config
+### **ccs_config**
 
 Contains the configuration files used by CIME to properly configure and build a CAM-SIMA (or CESM) case.  The Github repository associated with this directory can be found [here](https://github.com/ESMCI/ccs_config_cesm).
 
-### cime
+### **cime**
 
 Contains the [Common Infrastructure for Modeling the Earth (CIME)](https://github.com/ESMCI/cime) tools and associated libraries.  Used by CAM-SIMA and CESM for the general configuration and building of a simulation (or "case").
 
-### components
+### **components**
 
 Contains the following other CESM components:
 - [Community Data Models for Earth Prediction Systems (CDEPS)](https://github.com/ESCOMP/CDEPS)
@@ -37,21 +37,21 @@ Contains the following other CESM components:
 - [River Transport Model (RTM)](https://github.com/ESCOMP/RTM)
 
 
-### libraries
+### **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)
 
-### share
+### **share**
 
 Contains source code [shared across all CESM components](https://github.com/ESCOMP/CESM_share).
 
 ## Top-level CAM-SIMA directories
 
 These directories represent code and tools that is solely contained within the CAM-SIMA repository.  If there is a sub-directory that is also an external submodule or repository it will be marked with the "(external)" label.
 
-### cime_config
+### **cime_config**
 
 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.
 
@@ -60,15 +60,15 @@ Contains the SIMA-specific python and XML configuration routines used by CIME an
 - 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.
 
-### docker
+### **docker**
 
 Contains files needed to run certain CAM-SIMA configurations in a docker container.
 
-### src
+### **src**
 
 Contains all of the SIMA-specific source code needed to run the model. Additional details can be found below in the "Source directories" section.
 
-### test
+### **test**
 
 Contains everything needed to perform software testing and validation of CAM-SIMA source code.
 
@@ -78,31 +78,31 @@ Contains everything needed to perform software testing and validation of CAM-SIM
 - 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.
 
-### tools
+### **tools**
 
 Contains non-required scripts and source code that may be useful for CAM-SIMA development.
 
-## Source (src) directories
+## **Source (src) directories**
 
 This section lists all of the directories underneath the "src" top-level directory.
 
-### control
+### **control**
 
 Contains all of the source code needed for general model configuration, organization, and workflow, i.e. all of the "control" systems.
 
-### cpl
+### **cpl**
 
 Contains all of the source code needed for SIMA to interact with a coupler
 
 **Subdirectories**:
 
 - nuopc - Contains the source code needed to interact with the [NUOPC](https://earthsystemmodeling.org/nuopc/) coupler, which is brought in via the CMEPS external.
 
-### data
+### **data**
 
 Contains all of the source code needed to manage internal model data.  This includes auto-generated registry and initial conditions files code, physical constants, and atmospheric composition and thermodynamic properties.
 
-### dynamics
+### **dynamics**
 
 Contains all of the dynamical core (dycore) source code.
 
@@ -117,7 +117,7 @@ Contains all of the dynamical core (dycore) source code.
   - initial_conditions - Contains source code needed to configure specific analytic initial conditions formulations.
 - utils - Contains utility code used by all dycores in SIMA.
 
-### physics
+### **physics**
 
 Contains all of the SIMA physics and chemistry source code.
 
@@ -126,6 +126,6 @@ Contains all of the SIMA physics and chemistry source code.
 - ncar_ccpp (external) - External submodule that contains all of the code in the [atmospheric_physics](https://github.com/ESCOMP/atmospheric_physics) repo.
 - utils - Contains SIMA-specific utility routines for working with the CCPP-framework and CCPP-ized physics routines.
 
-### utils
+### **utils**
 
 Contains source code for generic SIMA utility routines that can be used throughout the model.