Liferay plugin projects are built using ant. When a new plugin project is created, there is one build.xml file created for the project. When you run ant on build.xml file, the process generates a war file and drops it in deploy folder of tomcat (or which ever is the hot deploy folder of your app server). Tomcat sees that there is a .war file in deploy folder and it immediately explodes it in webapps folder there by deploying the application.
liferay-plugin-packages.properties
If you want to use jar (or tld) files in your application that are already available with liferay portal then you can use liferay-plugin-packages.properties file to configure them. The build process will automatically bundle these jar files in the war file of your plugin project.
web.xml
The build process also regenerates the web.xml file with the required filters and servlets that participates in request processing for the portlets that are in your plugin project. The build process does preserve the changes you have done to your web.xml file in your project. After you deploy your project, check the contents of web.xml file in webapps/your-project/WEB-INF/web.xml. You will find many filters configured.
Fast deploy
When you configure Fast Deploy of jsps, you mention the docBase as the docroot folder in your plugins sdk/portlet/your-project. In fast deploy, the build process does not create a war file and does not deploy in webapps. Instead, it copies the context file in conf/catalina/localhost of your tomcat. When tomcat sees the file a new timestamp it reloads the context considering the source of your project (docroot) as the docBase. In such a case you will be able to see the contents of lib folder and contents of web.xml file in your project that is configured in eclipse
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