HashSets for starters.

src/engine/ConfigParsing/EffectEntry/Condition.java

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+package engine.ConfigParsing.EffectEntry;
+
+public class Condition {
+    public String type;
+    public String value;
+}

src/engine/ConfigParsing/EffectEntry/EffectEntry.java

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+package engine.ConfigParsing.EffectEntry;
+
+import java.util.HashSet;
+
+public class EffectEntry {
+    public String id;
+    public String name;
+    public int icon;
+    public HashSet<String> sources;
+    public HashSet<String> mods;
+    public HashSet<String> conditions;
+}

src/engine/ConfigParsing/EffectEntry/Mod.java

@@ -0,0 +1,10 @@
+package engine.ConfigParsing.EffectEntry;
+
+import engine.mbEnums;
+
+import java.util.ArrayList;
+
+public class Mod {
+    public mbEnums.ModType type;
+    public ArrayList<String> values;
+}