Those files you mention (.settings, .classpath, .project) are just metadata files from the IDE, and java does nothing with them, they are not part of a java project, the only thing you need to create a java program its a .java file. If you want to create a project, there are better ways, for example using maven https://maven.apache.org once you installed it, you can create a new project using the QuickStart archetype
mvn archetype:generate -DarchetypeGroupId=org.apache.maven.archetypes -DarchetypeArtifactId=maven-archetype-quickstart -DarchetypeVersion=1.4
It will create a standard structure for your project, and will save you a lot of work with the structure of your project, dependencies and build configurations.