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When you run "project > Build" , eclipse will compile all sources in folders on the build path to the .class files and put the .class files into the output folder you specified. Both of these folders can be configured from Project-> Properties-> Java Build Path . Note that eclipse has the incremental build feature that will only compile the sources that have changed since the last time the project is build.

If you enable Auto-build for the project ( via "Project-> Build Automatically" ) , the "project > Build" will run automatically when you add, remove, or modify the source files on the build path , so you don't have to call "project > Build" manually in this case.

The Publish option in the server tab will deploy the application to your Tomcat instance by copying the project resources such as xml configuration files , web resource (html ,css, js etc) , and the compiled .class files you get from the "project > Build" to the correct location of the Tomcat instance .

So , "Project > Build" is about compiling java sources to the .class files while the options in the server tab is about deploying the application to the tomcat instance and maintaining the tomcat instance .

You can find the information about the "server tab" (i.e. Web Tools Platform) from the following links:


Clean, Publish and Clean Tomcat Work directory options work on server files, on the other hand Project>build work on workspace files (projects are inside workspace folder). Server files and workspace files are usually in separated folders, it depends on how do you have configured your server.


Build: compile changed source files on the build path in the project
Clean: compile all source files on the build path in the project
Publish: Deploying the updated project in the web server instance

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