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I have an issue using LibGDX with assets directory. I actually build my project folder this way. I follow this tutorial to learn. (I work on Eclipse)
The code I use is :

package com.mygdx.game;

import com.badlogic.gdx.ApplicationListener;
import com.badlogic.gdx.Gdx;
import com.badlogic.gdx.graphics.GL20;
import com.badlogic.gdx.graphics.g2d.Sprite;
import com.badlogic.gdx.graphics.g2d.SpriteBatch;
import com.badlogic.gdx.graphics.g2d.TextureAtlas;
import com.badlogic.gdx.graphics.g2d.TextureAtlas.AtlasRegion;
import com.badlogic.gdx.utils.Timer;
import com.badlogic.gdx.utils.Timer.Task;

public class MyGdxGame implements ApplicationListener {
 private SpriteBatch batch;
 private TextureAtlas textureAtlas;
 private Sprite sprite;
 private int currentFrame = 1;
 private String currentAtlasKey = new String("0001");

 @Override
 public void create() 
 batch = new SpriteBatch();
 // THE PROBLEM IS UNDER THIS LINE
 textureAtlas = new TextureAtlas(Gdx.files.internal("spritesheet.atlas"));
 AtlasRegion region = textureAtlas.findRegion("0001");
 sprite = new Sprite(region);
 sprite.setPosition(120, 100);
 sprite.scale(2.5f);
 Timer.schedule(new Task()
 @Override
 public void run() 
 currentFrame++;
 if(currentFrame > 20)
 currentFrame = 1;

 // ATTENTION! String.format() doesnt work under GWT for god knows why...
 currentAtlasKey = String.format("%04d", currentFrame);
 sprite.setRegion(textureAtlas.findRegion(currentAtlasKey));
 
 
 ,0,1/30.0f);
 

 @Override
 public void dispose() 
 batch.dispose();
 textureAtlas.dispose();
 

 @Override
 public void render() 
 Gdx.gl.glClearColor(0, 0, 0, 1);
 Gdx.gl.glClear(GL20.GL_COLOR_BUFFER_BIT);

 batch.begin();
 sprite.draw(batch);
 batch.end();
 

 @Override
 public void resize(int width, int height) 
 

 @Override
 public void pause() 
 

 @Override
 public void resume() 
 

(if the code is hard to read I use exactly the same code that is in the tutorial linked below)

My package explorer looks like this :
imgur link

And it returns me :

Exception in thread "LWJGL Application" com.badlogic.gdx.utils.GdxRuntimeException: File not found: spritesheet.atlas (Internal)
at com.badlogic.gdx.files.FileHandle.read(FileHandle.java:136)
at com.badlogic.gdx.graphics.g2d.TextureAtlas$TextureAtlasData.(TextureAtlas.java:103)
at com.badlogic.gdx.graphics.g2d.TextureAtlas.(TextureAtlas.java:231)
at com.badlogic.gdx.graphics.g2d.TextureAtlas.(TextureAtlas.java:226)
at com.badlogic.gdx.graphics.g2d.TextureAtlas.(TextureAtlas.java:216)
at com.mygdx.game.MyGdxGame.create(MyGdxGame.java:23)
at com.badlogic.gdx.backends.lwjgl.LwjglApplication.mainLoop(LwjglApplication.java:149)
at com.badlogic.gdx.backends.lwjgl.LwjglApplication$1.run(LwjglApplication.java:126)

I tried some trick like Project>Clean, refreshing, close and re-open Eclipse and even recreated a project. Any idea ?

maybe you haven't linked the asset folder, if so,

try right click on my-gdx-game-desktop, in properties dialog select Java Build Path, click link source button, then navigate to the assets folder.

if you're already set it, try readd with this step, restart eclipse if needed

Okay, I found the trick. For those which encounter the same issue (working on Eclipse but it's pretty the same whatever the IDE is) there is one thread on stack overflow already existing which give additional solutions.
For me I had to set-up the "working directory" (for the desktop main for exemple). To do this go on Run>Run configuration>Arguments and at working directory's section there is Default and Other. Tick Other's box and me I had to write $workspace_loc:my-gdx-game-core/assets but I think it works like $workspace_loc:[name-of-your-core-directory]/assets. Hope it helped.