There are a good number of functions in the skills class. I want to brief you on things you should know. Firstly, skills has some static variables, or properties that are used as reference throughout the code source. These do not directly affect the character and instead are simply constants for doing things in the game. You will see skill IDs referred as either Skills.AGILITY or Constants.AGILITY, these can be used interchangeably and for any skill. All they are is numbers representing each skill, that is it.

Here are some examples of their usage at the bottom of their blocks...

public static ObjectClickHandler handleTrellis = new ObjectClickHandler(new Object[] { 20056 }, e -> {
	if (!Agility.hasLevel(e.getPlayer(), 18)) {
		e.getPlayer().sendMessage("You need 18 Agility to climb that.");
		return;
	}

	Player p = e.getPlayer();
	WorldObject obj = e.getObject();

	if(obj.getId() == 20056) {
		p.useLadder(WorldTile.of(2548, 3118, 1));
		p.getSkills().addXp(Skills.AGILITY, 31);
	}
});
	public static ObjectClickHandler handleAdvancedGnomeAgilityTree2 = new ObjectClickHandler(new Object[] { 69506 }, e -> {
		if (!Agility.hasLevel(e.getPlayer(), 85))
			return;
		e.getPlayer().sendMessage("You climb the tree...", true);
		e.getPlayer().useStairs(828, WorldTile.of(2472, 3419, 3), 1, 2, "... to the platform above.");
		if (getGnomeStage(e.getPlayer()) == 0)
			setGnomeStage(e.getPlayer(), 1);
		e.getPlayer().getSkills().addXp(Constants.AGILITY, 19);
	});

The reason there are two Java classes with these constants is just a lack of refactoring. Eventually we will be using Constants.java and that will be it. This is what they look like...

@PluginEventHandler  
public final class Skills {  
  private short level[];  
	private double xp[];
	
  public static final int
    ATTACK = 0, DEFENSE = 1,
    STRENGTH = 2, HITPOINTS = 3,
    RANGE = 4, PRAYER = 5,
    MAGIC = 6, COOKING = 7,
    WOODCUTTING = 8, FLETCHING = 9,
    FISHING = 10, FIREMAKING = 11,
    CRAFTING = 12, SMITHING = 13,
    MINING = 14, HERBLORE = 15,
    AGILITY = 16, THIEVING = 17,
    SLAYER = 18, FARMING = 19,
    RUNECRAFTING = 20, HUNTER = 21,
    CONSTRUCTION = 22, SUMMONING = 23,
    DUNGEONEERING = 24;
	
	public static final String[] SKILL_NAME = { "Attack", "Defence", "Strength", "Constitution", "Ranged", "Prayer", "Magic", "Cooking", "Woodcutting", "Fletching", "Fishing", "Firemaking", "Crafting", "Smithing", "Mining", "Herblore", "Agility",
			"Thieving", "Slayer", "Farming", "Runecrafting", "Hunter", "Construction", "Summoning", "Dungeoneering" };
  
	public void addXp(int skill, double exp) {  
    //...  
  }

 	public void set(int skill, int newLevel) {  
		level[skill] = (short) newLevel;  
		markForRefresh(skill);  
	}
  //etc...  
}
public class Constants {
    public static String CAPTCHA_SITE = "6Lfob18UAAAAAEx08Pvihg-vpSZ_wsFtG1aPotQw";
    public static String CAPTCHA_SECRET = "6Lfob18UAAAAAC1as5gXon-vEZYBdcLg7nt4pG3S";
    public static final String GRAB_SERVER_TOKEN = "ev9+VAp5/tMKeNR/7MOuH6lKWS+rGkHK";
    public static final String WORLD_TOKEN = "ev9+VAp5/tMKeNR/7MOuH6lKWS+rGkHK";
    public static final int[] GRAB_SERVER_KEYS = new int[]{1441, 78700, 44880, 39771, 363186, 44375, 0, 16140, 7316, 271148, 810710, 216189, 379672, 454149, 933950, 21006, 25367, 17247, 1244, 1, 14856, 1494, 119, 882901, 1818764, 3963, 3618};
    public static final BigInteger RSA_PRIVATE_MODULUS = new BigInteger("117525752735533423040644219776209926525585489242340044375332234679786347045466594509203355398209678968096551043842518449703703964361320462967286756268851663407950384008240524570966471744081769815157355561961607944067477858512067883877129283799853947605780903005188603658779539811385137666347647991072028080201");
    public static final BigInteger RSA_PRIVATE_EXPONENT = new BigInteger("45769714620275867926001532284788836149236590657678028481492967724067121406860916606777808563536714166085238449913676219414798301454048585933351540049893959827785868628572203706265915752274580525376826724019249600701154664022299724373133271944352291456503171589594996734220177420375212353960806722706846977073");
    public static final String SERVER_NAME = "Darkan";
    public static int CLIENT_BUILD = 727;
    public static int CUSTOM_CLIENT_BUILD = 1;
    public static int CLIENT_VERSION = 6;
    public static int PACKET_SIZE_LIMIT = 7500;
    public static final long WORLD_CYCLE_NS = 600000000L;
    public static final long WORLD_CYCLE_MS = 600L;
    public static final String[] SKILL_NAME = new String[]{"Attack", "Defence", "Strength", "Constitution", "Ranged", "Prayer", "Magic", "Cooking", "Woodcutting", "Fletching", "Fishing", "Firemaking", "Crafting", "Smithing", "Mining", "Herblore", "Agility", "Thieving", "Slayer", "Farming", "Runecrafting", "Hunter", "Construction", "Summoning", "Dungeoneering"};
    public static final int
      ATTACK = 0, DEFENSE = 1,
      STRENGTH = 2, HITPOINTS = 3,
      RANGE = 4, PRAYER = 5,
      MAGIC = 6, COOKING = 7,
      WOODCUTTING = 8, FLETCHING = 9,
      FISHING = 10, FIREMAKING = 11,
      CRAFTING = 12, SMITHING = 13,
      MINING = 14, HERBLORE = 15,
      AGILITY = 16, THIEVING = 17,
      SLAYER = 18, FARMING = 19,
      RUNECRAFTING = 20, HUNTER = 21,
      CONSTRUCTION = 22, SUMMONING = 23,
      DUNGEONEERING = 24;

    public Constants() {
    }
}