refactor: redesign plugin system and enhance message handling

- Move plugin and tool-related classes to a dedicated `Plugin-API` module.
- Introduce a new plugin lifecycle (`onInit`, `onEnable`, `onDisable`) and a more robust `Tool` API.
- Refactor `Core` to use `PrintAdvanceMessageHandler` for improved handling of assistant messages, tool responses, and errors.
- Rename `PluginLoader` to `Loader` and migrate it to `me.zacharias.chat.plugin.loader`.
- Update build configurations and Java toolchains across modules.
- Clean up obsolete plugin annotations and interfaces in the `Core` module.

Core/build.gradle

@@ -2,15 +2,29 @@ plugins {
     id 'java-library'
 }
 
-group = 'me.zacharias'
-version = '1.3'
+group = 'me.zacharias.neurodock'
+version = '1.5'
 
 dependencies {
-
+    implementation project(":Plugin-API")
+    api "org.json:json:20250107"
 }
 
 java {
     toolchain {
-        languageVersion.set(JavaLanguageVersion.of(21)) // Set Java version
+        languageVersion.set(JavaLanguageVersion.of(javaVersion)) // Set Java version
+    }
+}
+
+// Tell shadow not to interfere with the main publication
+shadowJar {
+    archiveClassifier = 'all'  // keeps shadow as -all.jar, not the main artifact
+}
+
+configurations {
+    [apiElements, runtimeElements].each {
+        it.outgoing.artifacts.removeIf {
+            it.buildDependencies.getDependencies(null).contains(shadowJar)
+        }
     }
 }

Core/src/main/java/me/zacharias/chat/core/Core.java

@@ -4,7 +4,7 @@ import me.zacharias.chat.core.memory.*;
 import me.zacharias.chat.ollama.*;
 import me.zacharias.chat.ollama.exceptions.OllamaToolErrorException;
 import me.zacharias.chat.plugin.Plugin;
-import me.zacharias.chat.plugin.PluginLoader;
+import me.zacharias.chat.plugin.loader.Loader;
 import me.zacharias.chat.plugin.exceptions.PluginLoadingException;
 import org.intellij.lang.annotations.MagicConstant;
 import org.jetbrains.annotations.NotNull;
@@ -68,11 +68,7 @@ public class Core {
     /**
      * The PrintMessageHandler to use.
      */
-    private final PrintMessageHandler printMessageHandler;
-    /**
-     * If color is supported by the PrintMessageHandler.
-     */
-    private boolean supportColor;
+    private final PrintAdvanceMessageHandler printMessageHandler;
 
     public static String DATA;
     public static File DATA_DIR;
@@ -234,9 +230,8 @@ public class Core {
      * Creates a new instance of Core with the provided PrintMessageHandler
      * @param printMessageHandler The PrintMessageHandler to use as the default Output
      */
-    public Core(@NotNull PrintMessageHandler printMessageHandler) {
+    public Core(@NotNull PrintAdvanceMessageHandler printMessageHandler) {
         this.printMessageHandler = printMessageHandler;
-        supportColor = printMessageHandler.color();
         ollamaIP = "localhost";
 
         // TODO: This is a dirty way to not have a masisive init block, please check this methods comment.
@@ -248,10 +243,9 @@ public class Core {
      * @param printMessageHandler The PrintMessageHandler to use as the default Output
      * @param ollamaIP            The IP used for the Ollama backend
      */
-    public Core(@NotNull PrintMessageHandler printMessageHandler, @NotNull String ollamaIP)
+    public Core(@NotNull PrintAdvanceMessageHandler printMessageHandler, @NotNull String ollamaIP)
     {
         this.printMessageHandler = printMessageHandler;
-        supportColor = printMessageHandler.color();
         this.ollamaIP = ollamaIP;
 
         // TODO: This is a dirty way to not have a masisive init block, please check this methods comment.
@@ -466,8 +460,9 @@ public class Core {
                             }
 
                             if(functions.isEmpty()) {
-                                ollamaObject.addMessage(new OllamaToolError("Function '"+function.getString("name")+"' does not exist"));
-                                printMessageHandler.printMessage((supportColor ?"\u001b[31m":"")+"Tried funtion call "+function.getString("name")+"("+deconstructOllamaFunctionArguments(argumentArrayList)+") but failed to find it."+(printMessageHandler.color()?"\u001b[0m":""));
+                                OllamaToolError ollamaToolError = new OllamaToolError("Function '" + function.getString("name") + "' does not exist");
+                                ollamaObject.addMessage(ollamaToolError);
+                                printMessageHandler.printErrorMessage(ollamaToolError);
                                 writeLog("Failed function call to "+function.getString("name"));
                             }
                             else {
@@ -479,11 +474,12 @@ public class Core {
                                 try {
                                     OllamaToolRespnce function1 = func.function(argumentArrayList.toArray(new OllamaFunctionArgument[0]));
                                     ollamaObject.addMessage(function1);
-                                    printMessageHandler.printMessage((supportColor?"\u001b[34m":"")+"Call "+func.name() + "(" + deconstructOllamaFunctionArguments(argumentArrayList) + ")" + (supportColor?"\u001b[0m":""));
+                                    printMessageHandler.printMessage(function1);
                                     writeLog("Successfully function call " + func.name() + " output: " + function1.getResponse());
                                 } catch (OllamaToolErrorException e) {
-                                    ollamaObject.addMessage(new OllamaToolError(e.getMessage()));
-                                    printMessageHandler.printMessage((supportColor?"\u001b[31m":"")+"Tried funtion call " + func.name() + "("+deconstructOllamaFunctionArguments(argumentArrayList)+") but failed due to " + e.getError() + (supportColor?"\u001b[0m":""));
+                                    OllamaToolError ollamaToolError = new OllamaToolError(e.getMessage());
+                                    ollamaObject.addMessage(ollamaToolError);
+                                    printMessageHandler.printErrorMessage(ollamaToolError);
                                     writeLog("ERROR: "+e.getMessage());
                                 }
                             }
@@ -505,9 +501,10 @@ public class Core {
         String message = responce.getJSONObject("message").getString("content");
         if(responce.getJSONObject("message").has("content") && !message.isBlank())
         {
-            printMessageHandler.printMessage((supportColor?"\u001b[32m":"")+(LaunchOptions.getInstance().isShowFullMessage()? message : message.replaceAll("(?s)<think>.*?</think>", "")) +(supportColor?"\u001b[0m":""));
+            OllamaMessage ollamaMessage = new OllamaMessage(OllamaMessageRole.ASSISTANT, message);
+            printMessageHandler.printMessage(ollamaMessage);
             writeLog("Response content: "+ message);
-            ollamaObject.addMessage(new OllamaMessage(OllamaMessageRole.ASSISTANT, message));
+            ollamaObject.addMessage(ollamaMessage);
         }
     }
     
@@ -541,7 +538,7 @@ public class Core {
         if(files == null) {
             return;
         }
-        PluginLoader loader = new PluginLoader();
+        Loader loader = new Loader();
         for(File file : files) {
             try(FileSystem fs = FileSystems.newFileSystem(file.toPath())){
                 if(!fs.getPath("/plugin.json").toFile().exists())

Core/src/main/java/me/zacharias/chat/core/PrintAdvanceMessageHandler.java

@@ -0,0 +1,25 @@
+package me.zacharias.chat.core;
+
+import me.zacharias.chat.ollama.OllamaMessage;
+import me.zacharias.chat.ollama.OllamaMessageRole;
+
+/**
+ * Represents a {@link PrintAdvanceMessageHandler}.
+ * This is used by the {@link Core} to print messages for the user, LLM, Tools, or potentialy System, see {@link OllamaMessageRole}.
+ * For a simpler version see {@link PrintMessageHandler}
+ */
+public interface PrintAdvanceMessageHandler {
+    /**
+     * Expected to handle the printing of the provided {@link OllamaMessage}.
+     * @param message The {@link OllamaMessage} requested to be printed from a veriity of sources, see {@link OllamaMessageRole}
+     */
+    void printMessage(OllamaMessage message);
+
+    /**
+     * Default method to print error messages to the user or API Client.
+     * This uses ANSI escape codes to color the output red if color is supported.
+     * @param errorMessage The error message to be printed.
+     * If color is not supported, it will print the message without color.
+     */
+    void printErrorMessage(OllamaMessage errorMessage);
+}

Core/src/main/java/me/zacharias/chat/core/PrintMessageHandler.java

@@ -1,16 +1,35 @@
 package me.zacharias.chat.core;
 
+import me.zacharias.chat.ollama.OllamaMessage;
+
+import static me.zacharias.chat.ollama.OllamaFunctionArgument.deconstructOllamaFunctionArguments;
+
 /**
  * Represents a PrintMessageHandler.
- * This is used by the Core to print messages to the user or API Clients.
+ * The Core uses this to print messages to the user or API Clients.
  */
-public interface PrintMessageHandler {
+public interface PrintMessageHandler extends PrintAdvanceMessageHandler {
     /**
      * Handles the printing of a message.
      * This is meant to output the message to the user or API Client.
      * @param message The message to be printed.
      */
     void printMessage(String message);
+
+    /**
+     * This is a default implementation when wrapping {@link PrintAdvanceMessageHandler} to this "simpler" {@link PrintMessageHandler}
+     *
+     *
+     * @param message The {@link OllamaMessage} requested to be printed from a veriity of sources, see {@link me.zacharias.chat.ollama.OllamaMessageRole}
+     */
+    default void printMessage(OllamaMessage message) {
+        printMessage(switch (message.getRole()) {
+            case ASSISTANT -> (color()?"\u001b[32m":"")+(LaunchOptions.getInstance().isShowFullMessage()? message.getContent() : message.getContent().replaceAll("(?s)<think>.*?</think>", "")) +(color()?"\u001b[0m":"");
+            case TOOL -> (color() ?"\u001b[31m":"")+message.getContent()+(color()?"\u001b[0m":"");
+            case USER, SYSTEM -> (color() ?"\u001b[37m":"")+message.getContent()+(color()?"\u001b[0m":"");
+            default -> throw new IllegalArgumentException("Invalid message role");
+        });
+    }
     
     /**
      * Gets if color is supported by the PrintMessageHandler.
@@ -32,4 +51,17 @@ public interface PrintMessageHandler {
             printMessage(message);
         }
     }
+
+    /**
+     * This is a default implementation when wrapping {@link PrintAdvanceMessageHandler} to this "simpler" {@link PrintMessageHandler}
+     *
+     *
+     * Default method to print error messages to the user or API Client.
+     * This uses ANSI escape codes to color the output red if color is supported.
+     * @param errorMessage The error message to be printed.
+     * If color is not supported, it will print the message without color.
+     */
+    default void printErrorMessage(OllamaMessage errorMessage) {
+        printError(errorMessage.getContent());
+    }
 }

Core/src/main/java/me/zacharias/chat/ollama/OllamaMessage.java

@@ -25,6 +25,20 @@ public class OllamaMessage {
         this.content = content;
     }
 
+    /**
+     * @return The role of who sent this "message", represented as {@link OllamaMessageRole}
+     */
+    public OllamaMessageRole getRole() {
+        return role;
+    }
+
+    /**
+     * @return The "message" or content sent by a source
+     */
+    public String getContent() {
+        return content;
+    }
+
     @Override
     public String toString() {
         JSONObject json = new JSONObject();

Core/src/main/java/me/zacharias/chat/ollama/OllamaObject.java

@@ -1,6 +1,5 @@
 package me.zacharias.chat.ollama;
 
-import com.sun.source.util.Plugin;
 import me.zacharias.chat.core.Core;
 import me.zacharias.chat.core.LaunchOptions;
 import me.zacharias.chat.core.Pair;
@@ -15,10 +14,6 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.lang.reflect.Field;
-import java.nio.file.FileSystem;
-import java.nio.file.FileSystems;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -452,6 +447,17 @@ public class OllamaObject {
             return this;
         }
 
+        /**
+         * Initializes the {@link FileHandler} singleton with the given base directory and adds its tools.
+         * <p>
+         * The {@link FileHandler} is intentionally constructed here rather than eagerly,
+         * as file access tooling should only be initialized if explicitly requested during
+         * object construction. Calling this after {@link #build()} is technically possible
+         * but not intended.
+         * </p>
+         * @param baseDirectory the base directory for file access, see {@link FileHandlerLocation}
+         * @return The {@link OllamaObjectBuilder}
+         */
         public OllamaObjectBuilder addFileTools(@MagicConstant(valuesFromClass = FileHandlerLocation.class) String baseDirectory)
         {
             new FileHandler(baseDirectory);

Core/src/main/java/me/zacharias/chat/plugin/Plugin.java

@@ -1,5 +0,0 @@
-package me.zacharias.chat.plugin;
-
-public class Plugin {
-    private final PluginMetadata metadata = null;
-}

Core/src/main/java/me/zacharias/chat/plugin/PluginLoader.java

@@ -1,62 +0,0 @@
-package me.zacharias.chat.plugin;
-
-import org.json.JSONObject;
-
-import java.lang.reflect.Field;
-import java.nio.file.FileSystem;
-import java.nio.file.Path;
-
-public class PluginLoader {
-
-    public PluginLoader() {
-    }
-
-    public Plugin loadPlugin(FileSystem pluginJar, JSONObject pluginMeta) throws ClassNotFoundException, IllegalAccessException, InstantiationException {
-        String pluginName = pluginMeta.getString("name");
-        String pluginEntryPoint = pluginMeta.getString("entryPoint");
-        String pluginVersion = pluginMeta.getString("version");
-        String pluginDescription = pluginMeta.optString("description", "No description provided");
-        String[] pluginAuthors = pluginMeta.optJSONArray("author") != null ?
-            pluginMeta.getJSONArray("author").toList().toArray(new String[0]) : new String[0];
-
-        PluginMetadata pluginMetadata = new PluginMetadata() {
-            @Override
-            public String getName() {
-                return pluginName;
-            }
-
-            @Override
-            public String getVersion() {
-                return pluginVersion;
-            }
-
-            @Override
-            public String getDescription() {
-                return pluginDescription;
-            }
-
-            @Override
-            public String[] getAuthor() {
-                return pluginAuthors;
-            }
-
-            @Override
-            public String entryPoint() {
-                return pluginEntryPoint;
-            }
-        };
-
-        try {
-            Plugin plugin = (Plugin) Class.forName(pluginEntryPoint).newInstance();
-            Field metadataField = plugin.getClass().getDeclaredField("metadata");
-            metadataField.set(plugin, pluginMetadata);
-            if (metadataField.get(plugin) == null)
-                throw new IllegalStateException("Plugin metadata field is null for plugin: " + pluginName);
-        }catch (NoSuchFieldException e)
-        {
-            throw new IllegalStateException("Plugin class " + pluginEntryPoint + " does not have a 'metadata' field", e);
-        }
-        return null;
-        //ClassLoader classLoader = pluginJar.
-    }
-}

Core/src/main/java/me/zacharias/chat/plugin/PluginMetadata.java

@@ -1,9 +0,0 @@
-package me.zacharias.chat.plugin;
-
-public interface PluginMetadata {
-    public String getName();
-    public String getVersion();
-    public String getDescription();
-    public String[] getAuthor();
-    public String entryPoint();
-}

Core/src/main/java/me/zacharias/chat/plugin/annotation/OllamaTool.java

@@ -1,12 +0,0 @@
-package me.zacharias.chat.plugin.annotation;
-
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-
-@Retention(RetentionPolicy.RUNTIME)
-@Target(ElementType.TYPE)
-public @interface OllamaTool {
-
-}

Core/src/main/java/me/zacharias/chat/plugin/annotation/injectons/InjectPlugin.java

@@ -1,14 +0,0 @@
-package me.zacharias.chat.plugin.annotation.injectons;
-
-import me.zacharias.chat.plugin.Plugin;
-
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-
-@Retention(RetentionPolicy.RUNTIME)
-@Target({ElementType.FIELD, ElementType.PARAMETER, ElementType.METHOD})
-public @interface InjectPlugin {
-    Class<? extends Plugin> classType() default Plugin.class;
-}

Core/src/main/java/me/zacharias/chat/plugin/exceptions/PluginLoadingException.java

@@ -1,7 +0,0 @@
-package me.zacharias.chat.plugin.exceptions;
-
-public class PluginLoadingException extends RuntimeException {
-    public PluginLoadingException(String message, String pluginName) {
-        super("Plugin: \""+pluginName+"\"> "+message);
-    }
-}

Core/src/main/java/me/zacharias/chat/plugin/loader/Loader.java

@@ -0,0 +1,62 @@
+package me.zacharias.chat.plugin.loader;
+
+import jdk.jshell.spi.ExecutionControl;
+import me.zacharias.chat.core.Pair;
+import me.zacharias.chat.ollama.*;
+import me.zacharias.chat.plugin.Plugin;
+import me.zacharias.chat.plugin.PluginMetadata;
+import me.zacharias.chat.plugin.exceptions.ToolRuntimeException;
+import me.zacharias.chat.plugin.tool.Tool;
+import me.zacharias.chat.plugin.tool.ToolResponse;
+import org.jetbrains.annotations.NotNull;
+
+import java.util.ArrayList;
+
+public class Loader {
+    private final ArrayList<Pair<Plugin, PluginMetadata>> plugins = new ArrayList<>();
+
+    /**
+     * Mock example!
+     * @return
+     */
+    public OllamaTool getTool() {
+        // Mock example!
+        Tool tool = null;
+
+        return new OllamaFunctionTool() {
+            @Override
+            public @NotNull String name() {
+                return tool.name();
+            }
+
+            @Override
+            public String description() {
+                return tool.description();
+            }
+
+            @Override
+            public @NotNull OllamaPerameter parameters() {
+                // TODO: make a wrapper around ToolPerameters to OllamaPeramer
+                throw new RuntimeException(new ExecutionControl.NotImplementedException("To be Implemented"));
+            }
+
+            @Override
+            public OllamaToolRespnce function(OllamaFunctionArgument... args) {
+                // Wrap OllamaFunctionArguments[] to ether ToolArgument[] or ToolArguments(current implementation)
+                try {
+                    ToolResponse toolResponse = tool.callTool(null);
+                } catch (ToolRuntimeException e) {
+                    throw new RuntimeException(e);
+                }
+                // Wrap ToolResponce to an OllamaToolRespnce(Well I see a typo here now)
+                return null;
+            }
+
+            @Override
+            public String toString() {
+                // Replaces the toString which is used thru out the Core and OllamaObject to get the JSON representation of a Function Tool
+                return tool.getToolJSON();
+            }
+        };
+    }
+}

Core/src/test/java/plugin/Tool.java

@@ -6,6 +6,7 @@ import me.zacharias.chat.ollama.OllamaPerameter;
 import me.zacharias.chat.ollama.OllamaToolRespnce;
 import me.zacharias.chat.plugin.annotation.OllamaTool;
 import me.zacharias.chat.plugin.annotation.injectons.InjectPlugin;
+import org.jetbrains.annotations.NotNull;
 
 @OllamaTool
 public class Tool extends OllamaFunctionTool {
@@ -13,7 +14,7 @@ public class Tool extends OllamaFunctionTool {
     Test core;
 
     @Override
-    public String name() {
+    public @NotNull String name() {
         return "";
     }
 
@@ -23,7 +24,7 @@ public class Tool extends OllamaFunctionTool {
     }
 
     @Override
-    public OllamaPerameter parameters() {
+    public @NotNull OllamaPerameter parameters() {
         return null;
     }