Update Alchemy for 1.9 Configuration style has changed, but theoretically old version should still work I think.

src/main/java/com/gmail/nossr50/config/skills/alchemy/PotionConfig.java

@@ -28,7 +28,7 @@ public class PotionConfig extends ConfigLoader {
     private List<ItemStack> concoctionsIngredientsTierSeven = new ArrayList<ItemStack>();
     private List<ItemStack> concoctionsIngredientsTierEight = new ArrayList<ItemStack>();
 
-    private Map<Short, AlchemyPotion> potionMap = new HashMap<Short, AlchemyPotion>();
+    private Map<String, AlchemyPotion> potionMap = new HashMap<String, AlchemyPotion>();
 
     private PotionConfig() {
         super("potions.yml");
@@ -90,11 +90,11 @@ public class PotionConfig extends ConfigLoader {
         int pass = 0;
         int fail = 0;
 
-        for (String dataValue : potionSection.getKeys(false)) {
-            AlchemyPotion potion = loadPotion(potionSection.getConfigurationSection(dataValue));
+        for (String potionName : potionSection.getKeys(false)) {
+            AlchemyPotion potion = loadPotion(potionSection.getConfigurationSection(potionName));
 
             if (potion != null) {
-                potionMap.put(potion.getDataValue(), potion);
+                potionMap.put(potionName, potion);
                 pass++;
             }
             else {
@@ -115,12 +115,20 @@ public class PotionConfig extends ConfigLoader {
      */
     private AlchemyPotion loadPotion(ConfigurationSection potion_section) {
         try {
-            short dataValue = Short.parseShort(potion_section.getName());
+            
 
             String name = potion_section.getString("Name");
             if (name != null) {
                 name = ChatColor.translateAlternateColorCodes('&', name);
             }
+            
+            short dataValue = Short.parseShort(potion_section.getString("Data"));
+            
+            Material material = Material.POTION;
+            String mat = potion_section.getString("Material", null);
+            if (mat != null) {
+                material = Material.valueOf(mat);
+            }
 
             List<String> lore = new ArrayList<String>();
             if (potion_section.contains("Lore")) {
@@ -147,12 +155,12 @@ public class PotionConfig extends ConfigLoader {
                 }
             }
 
-            Map<ItemStack, Short> children = new HashMap<ItemStack, Short>();
+            Map<ItemStack, String> children = new HashMap<ItemStack, String>();
             if (potion_section.contains("Children")) {
                 for (String child : potion_section.getConfigurationSection("Children").getKeys(false)) {
                     ItemStack ingredient = loadIngredient(child);
                     if (ingredient != null) {
-                        children.put(ingredient, Short.parseShort(potion_section.getConfigurationSection("Children").getString(child)));
+                        children.put(ingredient, potion_section.getConfigurationSection("Children").getString(child));
                     }
                     else {
                         mcMMO.p.getLogger().warning("Failed to parse child for potion " + name + ": " + child);
@@ -160,7 +168,7 @@ public class PotionConfig extends ConfigLoader {
                 }
             }
 
-            return new AlchemyPotion(dataValue, name, lore, effects, children);
+            return new AlchemyPotion(material, dataValue, name, lore, effects, children);
         }
         catch (Exception e) {
             mcMMO.p.getLogger().warning("Failed to load Alchemy potion: " + potion_section.getName());
@@ -220,7 +228,16 @@ public class PotionConfig extends ConfigLoader {
         return potionMap.containsKey(item.getDurability());
     }
 
-    public AlchemyPotion getPotion(short durability) {
-        return potionMap.get(durability);
+    public AlchemyPotion getPotion(String name) {
+        return potionMap.get(name);
+    }
+    
+    public AlchemyPotion getPotion(ItemStack item) {
+        for (AlchemyPotion potion : potionMap.values()) {
+            if (potion.isSimilar(item)) {
+                return potion;
+            }
+        }
+        return null;
     }
 }

src/main/java/com/gmail/nossr50/datatypes/skills/alchemy/AlchemyPotion.java

@@ -10,14 +10,18 @@ import org.bukkit.inventory.meta.PotionMeta;
 import org.bukkit.potion.Potion;
 import org.bukkit.potion.PotionEffect;
 
+import com.gmail.nossr50.config.skills.alchemy.PotionConfig;
+
 public class AlchemyPotion {
+    private Material material;
     private short dataValue;
     private String name;
     private List<String> lore;
     private List<PotionEffect> effects;
-    private Map<ItemStack, Short> children;
+    private Map<ItemStack, String> children;
 
-    public AlchemyPotion(short dataValue, String name, List<String> lore, List<PotionEffect> effects, Map<ItemStack, Short> children) {
+    public AlchemyPotion(Material material, short dataValue, String name, List<String> lore, List<PotionEffect> effects, Map<ItemStack, String> children) {
+        this.material = material;
         this.dataValue = dataValue;
         this.lore = lore;
         this.name = name;
@@ -30,7 +34,7 @@ public class AlchemyPotion {
     }
 
     public ItemStack toItemStack(int amount) {
-        ItemStack potion = new ItemStack(Material.POTION, amount, this.getDataValue());
+        ItemStack potion = new ItemStack(material, amount, this.getDataValue());
         PotionMeta meta = (PotionMeta) potion.getItemMeta();
 
         if (this.getName() != null) {
@@ -51,6 +55,10 @@ public class AlchemyPotion {
         return potion;
     }
 
+    public Material getMaterial() {
+        return material;
+    }
+
     public Potion toPotion(int amount) {
         return Potion.fromItemStack(this.toItemStack(amount));
     }
@@ -87,22 +95,50 @@ public class AlchemyPotion {
         this.effects = effects;
     }
 
-    public Map<ItemStack, Short> getChildren() {
+    public Map<ItemStack, String> getChildren() {
         return children;
     }
 
-    public void setChildren(Map<ItemStack, Short> children) {
+    public void setChildren(Map<ItemStack, String> children) {
         this.children = children;
     }
 
-    public Short getChildDataValue(ItemStack ingredient) {
+    public AlchemyPotion getChild(ItemStack ingredient) {
         if (!children.isEmpty()) {
-            for (Entry<ItemStack, Short> child : children.entrySet()) {
+            for (Entry<ItemStack, String> child : children.entrySet()) {
                 if (ingredient.isSimilar(child.getKey())) {
-                    return child.getValue();
+                    return PotionConfig.getInstance().getPotion(child.getValue());
                 }
             }
         }
-        return -1;
+        return null;
+    }
+
+    public boolean isSimilar(ItemStack item) {
+        if (item.getType() != material) {
+            return false;
+        }
+        if (item.getDurability() != dataValue) {
+            return false;
+        }
+        if (!item.hasItemMeta()) {
+            return false;
+        }
+        PotionMeta meta = (PotionMeta) item.getItemMeta();
+        for (PotionEffect effect : effects) {
+            if (!meta.hasCustomEffect(effect.getType())) {
+                return false;
+            }
+        }
+        if (!meta.hasLore()) {
+            return false;
+        }
+        if (!meta.getLore().equals(lore)) {
+            return false;
+        }
+        if (!meta.hasDisplayName()) {
+            return false;
+        }
+        return meta.getDisplayName().equals(name);
     }
 }

src/main/java/com/gmail/nossr50/skills/alchemy/AlchemyPotionBrewer.java

@@ -36,7 +36,7 @@ public final class AlchemyPotionBrewer {
                 continue;
             }
 
-            if (getChildPotion(PotionConfig.getInstance().getPotion(contents[i].getDurability()), contents[Alchemy.INGREDIENT_SLOT]) != null) {
+            if (getChildPotion(PotionConfig.getInstance().getPotion(contents[i]), contents[Alchemy.INGREDIENT_SLOT]) != null) {
                 return true;
             }
         }
@@ -45,8 +45,8 @@ public final class AlchemyPotionBrewer {
     }
 
     private static AlchemyPotion getChildPotion(AlchemyPotion potion, ItemStack ingredient) {
-        if (potion != null && potion.getChildDataValue(ingredient) != -1) {
-            return PotionConfig.getInstance().getPotion(potion.getChildDataValue(ingredient));
+        if (potion != null) {
+            return potion.getChild(ingredient);
         }
 
         return null;
@@ -118,8 +118,8 @@ public final class AlchemyPotionBrewer {
                 continue;
             }
 
-            AlchemyPotion input = PotionConfig.getInstance().getPotion(item.getDurability());
-            AlchemyPotion output = PotionConfig.getInstance().getPotion(input.getChildDataValue(ingredient));
+            AlchemyPotion input = PotionConfig.getInstance().getPotion(item);
+            AlchemyPotion output = input.getChild(ingredient);
 
             inputList.add(input);
 
@@ -138,7 +138,7 @@ public final class AlchemyPotionBrewer {
         removeIngredient(inventory, player);
 
         for (AlchemyPotion input : inputList) {
-            AlchemyPotion output = PotionConfig.getInstance().getPotion(input.getChildDataValue(ingredient));
+            AlchemyPotion output = input.getChild(ingredient);
 
             if (output != null && player != null) {
                 PotionStage potionStage = PotionStage.getPotionStage(input, output);

src/main/resources/potions.yml

@@ -63,9 +63,12 @@ Potions:
 
     ### NON-EFFECT POTIONS #####################################################
 
-    0: # Water Bottle
+    WATER: # Water Bottle
+        Name: Water Bottle
+        Material: POTION
+        Data: 0
         Children:
-            BLAZE_POWDER: 8192          # Mundane Potion
+            BLAZE_POWDER: MUNDANE_POTION
             FERMENTED_SPIDER_EYE: 8200  # Potion of Weakness
             GHAST_TEAR: 8192            # Mundane Potion
             GLOWSTONE_DUST: 32          # Thick Potion
@@ -77,6 +80,8 @@ Potions:
             SUGAR: 8192                 # Mundane Potion
 
     16: # Awkward Potion
+        Material: POTION
+        Data: 0
         Children:
             APPLE: 5376                 # Potion of Health Boost
             BLAZE_POWDER: 8201          # Potion of Strength