--------Issue 1--------
While clicking on Run or Debug for the first time after configuring tomcat server:
You may get this error:
Could not find or load main class org.apache.catalina.startup.Bootstrap
See the following configuration.
You need to add the Program arguments and VM arguments as:

Program arguments:
start
VM arguments:
-Dcatalina.base="C:\Users\ID\Documents\TCS_GE_Confidential\Project\Master_branch\.metadata\.plugins\org.eclipse.wst.server.core\tmp0" -Dcatalina.home="C:\Users\ID\Documents\TCS Internal\Softwares\apache-tomcat-8.0.9-windows-x86\apache-tomcat-8.0.9" -Dwtp.deploy="C:\Users\ID\Documents\TCS_GE_Confidential\Project\Master_branch\.metadata\.plugins\org.eclipse.wst.server.core\tmp0\wtpwebapps" -Djava.endorsed.dirs="C:\Users\ID\Documents\TCS Internal\Softwares\apache-tomcat-8.0.9-windows-x86\apache-tomcat-8.0.9\endorsed"
And add these JARs to the classpath:

--------Issue 2--------
You might not be able to see the Tomcat server v8.0 or any version (i.e configured Runtime environment) in your eclipse/STSwhen you open the Debug configuration or Run configuration.
The section shown in the following snapshot might be might in your case.

Solution:
Just right click on the Servers in your Project explorer/Navigator:New > Other > Server > Server.

Click Finish.
If you are not able to see your server here also, then you need to add it to the Server runtime environment by going to Window > Preferences > Server > Runtime Environment > Add
While clicking on Run or Debug for the first time after configuring tomcat server:
You may get this error:
Could not find or load main class org.apache.catalina.startup.Bootstrap
See the following configuration.
You need to add the Program arguments and VM arguments as:

Program arguments:
start
VM arguments:
-Dcatalina.base="C:\Users\ID\Documents\TCS_GE_Confidential\Project\Master_branch\.metadata\.plugins\org.eclipse.wst.server.core\tmp0" -Dcatalina.home="C:\Users\ID\Documents\TCS Internal\Softwares\apache-tomcat-8.0.9-windows-x86\apache-tomcat-8.0.9" -Dwtp.deploy="C:\Users\ID\Documents\TCS_GE_Confidential\Project\Master_branch\.metadata\.plugins\org.eclipse.wst.server.core\tmp0\wtpwebapps" -Djava.endorsed.dirs="C:\Users\ID\Documents\TCS Internal\Softwares\apache-tomcat-8.0.9-windows-x86\apache-tomcat-8.0.9\endorsed"
And add these JARs to the classpath:

--------Issue 2--------
You might not be able to see the Tomcat server v8.0 or any version (i.e configured Runtime environment) in your eclipse/STSwhen you open the Debug configuration or Run configuration.
The section shown in the following snapshot might be might in your case.

Solution:
Just right click on the Servers in your Project explorer/Navigator:New > Other > Server > Server.

Click Finish.
If you are not able to see your server here also, then you need to add it to the Server runtime environment by going to Window > Preferences > Server > Runtime Environment > Add
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