The new project does not have a workaround for the Src/main/java and src/main/resources two source files:
Step 1:create a Maven Webapp project. Right click on the package Explorer pane go to new–> Maven Project
Step 2:select the archetype as "Maven-archetype-webapp" and click on Next and give the artifact ID as "HelloWorld".
Step 3:after You create a MAVEN Web App project and you'll be have the Web project created like below. Now we can, the HelloWorld Project doesn ' t has Src/main/java and Src/test/java folders in it. It has only the Src/main/resource folder.
Step 4:even When do try to create a new Source folder you'll be getting the error like "The folder is already a sour Ce folder ".
Step 5:fixing This issue are very simple and right Click on the project go to Properties. In this go to Build path, you'll be the having a error like "2 Build path entries is missing"
Step 6:this error usually occurs where the JRE System Library is wrongly pointed. Now go to Libraries tab and change the JRE System Library to the correct version.
Step 7:once The JRE System Library is changed the issue should being resolved, all of you need to do are to does an Update PROJEC T (right on the project–> maven–> Update Project). Now you should has the Src/main/java and Src/test/java folders.
Happy Learning!! ??
Source: http://www.javainterviewpoint.com/missing-srcmainjava-folder-eclipse-maven/
Fix missing Src/main/java folder in Eclipse Maven project–2 build path entries is missing