When you want to start developing an application, make sure to organise your files into packages, sub-packages, and classes. This organisation can help you understand each part usages and decreases debugging time.
For example if you want to create a rest-api in Java, you can use the following structure:
|_ lib/
|_ server/
|_ src/
|_ main/
|_ controller/
|_ UserController.java
|_ model/
|_ User.java
|_ url/
|_ Http.java
|_ Request.java
|_ Response.java
|_ pom.xml
|_ config.txt
|_ database
|_ src/
|_ main/
|_ query
|_ User.java
|_ guid.txt