Shit has happend, among the "shit" is working on the files stuff and refactoring Core.Source to reflect on the new names for the difrent types of tool sources

.idea/misc.xml

@@ -7,6 +7,45 @@
   <component name="FrameworkDetectionExcludesConfiguration">
     <file type="web" url="file://$PROJECT_DIR$" />
   </component>
+  <component name="NullableNotNullManager">
+    <option name="myDefaultNullable" value="org.jetbrains.annotations.Nullable" />
+    <option name="myDefaultNotNull" value="org.jetbrains.annotations.NotNull" />
+    <option name="myOrdered" value="false" />
+    <option name="myNullables">
+      <value>
+        <list size="11">
+          <item index="0" class="java.lang.String" itemvalue="org.jspecify.annotations.Nullable" />
+          <item index="1" class="java.lang.String" itemvalue="org.jetbrains.annotations.Nullable" />
+          <item index="2" class="java.lang.String" itemvalue="org.checkerframework.checker.nullness.qual.Nullable" />
+          <item index="3" class="java.lang.String" itemvalue="org.checkerframework.checker.nullness.compatqual.NullableDecl" />
+          <item index="4" class="java.lang.String" itemvalue="org.checkerframework.checker.nullness.compatqual.NullableType" />
+          <item index="5" class="java.lang.String" itemvalue="org.eclipse.jdt.annotation.Nullable" />
+          <item index="6" class="java.lang.String" itemvalue="edu.umd.cs.findbugs.annotations.Nullable" />
+          <item index="7" class="java.lang.String" itemvalue="jakarta.annotation.Nullable" />
+          <item index="8" class="java.lang.String" itemvalue="javax.annotation.Nullable" />
+          <item index="9" class="java.lang.String" itemvalue="javax.annotation.CheckForNull" />
+          <item index="10" class="java.lang.String" itemvalue="org.springframework.lang.Nullable" />
+        </list>
+      </value>
+    </option>
+    <option name="myNotNulls">
+      <value>
+        <list size="11">
+          <item index="0" class="java.lang.String" itemvalue="org.jspecify.annotations.NonNull" />
+          <item index="1" class="java.lang.String" itemvalue="org.jetbrains.annotations.NotNull" />
+          <item index="2" class="java.lang.String" itemvalue="org.checkerframework.checker.nullness.qual.NonNull" />
+          <item index="3" class="java.lang.String" itemvalue="org.checkerframework.checker.nullness.compatqual.NonNullDecl" />
+          <item index="4" class="java.lang.String" itemvalue="org.checkerframework.checker.nullness.compatqual.NonNullType" />
+          <item index="5" class="java.lang.String" itemvalue="org.eclipse.jdt.annotation.NonNull" />
+          <item index="6" class="java.lang.String" itemvalue="edu.umd.cs.findbugs.annotations.NonNull" />
+          <item index="7" class="java.lang.String" itemvalue="jakarta.annotation.Nonnull" />
+          <item index="8" class="java.lang.String" itemvalue="javax.annotation.Nonnull" />
+          <item index="9" class="java.lang.String" itemvalue="lombok.NonNull" />
+          <item index="10" class="java.lang.String" itemvalue="org.springframework.lang.NonNull" />
+        </list>
+      </value>
+    </option>
+  </component>
   <component name="ProjectRootManager" version="2" languageLevel="JDK_26" default="true" project-jdk-name="26" project-jdk-type="JavaSDK">
     <output url="file://$PROJECT_DIR$/out" />
   </component>

Core/src/main/java/me/neurodock/core/Core.java

@@ -74,6 +74,36 @@ public class Core {
     public static File PLUGIN_DIRECTORY;
     public static File CACHE_DIRECTORY;
 
+    /**
+     * Creates a new instance of Core with the provided PrintMessageHandler,
+     * defaulting the Ollama backend to {@code localhost}.
+     *
+     * @param printMessageHandler The PrintMessageHandler to use as the default output
+     */
+    public Core(@NotNull PrintAdvanceMessageHandler printMessageHandler) {
+        this(printMessageHandler, "localhost");
+    }
+
+    /**
+     * Creates a new instance of Core with the provided PrintMessageHandler
+     * and a specific Ollama backend address.
+     *
+     * @param printMessageHandler The PrintMessageHandler to use as the default output
+     * @param ollamaIP            The IP or hostname of the Ollama backend
+     */
+    public Core(@NotNull PrintAdvanceMessageHandler printMessageHandler, @NotNull String ollamaIP)
+    {
+        this.printMessageHandler = printMessageHandler;
+        this.ollamaIP = ollamaIP;
+
+        initDirectories();
+        initOllamaUrl();
+        confirmOllama();
+        initLogWriter();
+        initScheduler();
+        initShutdownHook();
+    }
+
     static {
         // This should not be enforced like this, instead this should read a data field, or wait for an init to be called....
         // Unsure of how to properly do this at this time, however.
@@ -407,6 +437,7 @@ public class Core {
     private void confirmOllama()
     {
         try {
+            URL url = new URL("http://" + ollamaIP + ":" + ollamaPort + "/api/version");
             HttpURLConnection connection = (HttpURLConnection) url.openConnection();
             connection.setRequestMethod("GET");
             connection.setRequestProperty("Content-Type", "application/json");
@@ -427,36 +458,6 @@ public class Core {
         }
     }
 
-    /**
-     * Creates a new instance of Core with the provided PrintMessageHandler,
-     * defaulting the Ollama backend to {@code localhost}.
-     *
-     * @param printMessageHandler The PrintMessageHandler to use as the default output
-     */
-    public Core(@NotNull PrintAdvanceMessageHandler printMessageHandler) {
-        this(printMessageHandler, "localhost");
-    }
-
-    /**
-     * Creates a new instance of Core with the provided PrintMessageHandler
-     * and a specific Ollama backend address.
-     *
-     * @param printMessageHandler The PrintMessageHandler to use as the default output
-     * @param ollamaIP            The IP or hostname of the Ollama backend
-     */
-    public Core(@NotNull PrintAdvanceMessageHandler printMessageHandler, @NotNull String ollamaIP)
-    {
-        this.printMessageHandler = printMessageHandler;
-        this.ollamaIP = ollamaIP;
-
-        initDirectories();
-        initOllamaUrl();
-        confirmOllama();
-        initLogWriter();
-        initScheduler();
-        initShutdownHook();
-    }
-
     /**
      * Sets the {@link #ollamaObject} object to the provided argument,
      * Also adds the memory base system. See {@link Core#setOllamaObjectNoMemory} if you don't want to add memory functions
@@ -768,31 +769,29 @@ public class Core {
      * Represents the source of a tool.
      * <p>
      * This is intended for use with {@link Core#addTool(OllamaFunctionTool, String)}
-     * to indicate the module from which a tool originates.
+     * to indicate the category from which a tool originates.
      */
     public static class Source {
         /**
-         * Represents an external tool that is not derived from the Core.
-         * Instead, it belongs to an internally defined system or module within the project/program.
-         */
-        public static final String EXTERNAL = "External";
-        
-        /**
-         * Represents an internally defined tool that is part of the Core system.
-         * This is meant for tools that are strictly part of the Core and should not be used for definitions outside of it.
+         * Tools boundeld with the Core runtime (memory, file access, etc.)
+         * DO NOT USE THIS unless you are poking at core stuff :).
          */
         public static final String CORE = "Core";
 
         /**
-         * Represents a tool defined through an API system.
-         * These tools are more dynamic, as they originate from fully external sources using the API.
+         * Compile-Time Plugins: boundeld at build time as part of the application.
+         * Examples: MALAPITool, GeniusAPI, WikipediaTool.
          */
-        public static final String API = "Api";
+        public static final String CTP = "CTP";
 
         /**
-         * Represents an internally defined tool that is derived from Core Components but not the Core itself.
-         * This is used for tools that are part of the Core Components, such as internal modules, but do not belong directly to the Core.
+         * Runtime Pre-Compiled Plugins: external plugins loaded at runtime via Plugin-API.
          */
-        public static final String INTERNAL = "Internal";
+        public static final String RPCP = "RPCP";
+
+        /**
+         * Tools defined via the RESt API interface dynamically.
+         */
+        public static final String API = "API";
     }
 }

Core/src/main/java/me/neurodock/core/files/FileHandler.java

@@ -54,7 +54,7 @@ public class FileHandler {
     public static ArrayList<Pair<? extends OllamaTool, String>> getTools() {
         ArrayList<Pair<? extends OllamaTool, String>> tools = new ArrayList<>();
 
-        tools.add(new Pair<>(new ReadFileTool(), Core.Source.INTERNAL));
+        tools.add(new Pair<>(new ReadFileTool(), Core.Source.CORE));
 
         return tools;
     }

Core/src/main/java/me/neurodock/core/files/tools/ReadFileTool.java

@@ -26,7 +26,7 @@ public class ReadFileTool extends OllamaFunctionTool {
     @Override
     public @NotNull OllamaPerameter parameters() {
         return OllamaPerameter.builder()
-                .addProperty("file_path", OllamaPerameter.OllamaPerameterBuilder.Type.STRING, "The path to the file to be read")
+                .addProperty("file_path", OllamaPerameter.OllamaPerameterBuilder.Type.STRING, "The path to the file to be read", true)
                 .build();
     }
 

Core/src/main/java/me/neurodock/core/memory/CoreMemory.java

@@ -70,6 +70,10 @@ public class CoreMemory {
                 e.printStackTrace();
             }
         }
+        else {
+            memory.put(MAPPED_MEMORY, new JSONObject());
+            memory.put(ARRAYED_MEMORY, new JSONArray());
+        }
 
         this.memoryFile = memoryFile;
 

Core/src/main/java/me/neurodock/ollama/OllamaFunctionTools.java

@@ -53,7 +53,7 @@ public class OllamaFunctionTools implements Iterable<Pair<OllamaFunctionTool, St
         }
 
         for (String s : source) {
-            if (s.equals(Core.Source.INTERNAL)) {
+            if (s.equals(Core.Source.CTP)) {
                 this.source.add(s);
             }
         }

Core/src/main/java/me/neurodock/ollama/OllamaObject.java

@@ -69,6 +69,32 @@ public class OllamaObject {
     private OllamaObject(String model, ArrayList<OllamaMessage> messages, ArrayList<Pair<OllamaTool, String>> tools, JSONObject format, Map<String, Object> options, boolean stream, String keep_alive) {
         this.model = model;
         this.messages = messages;
+
+        // Reflecting the reflection injection for ALL tools that was added in the OllamaObjectBuilder, etc, etc comment.. its past midnignt and i'm tired.
+        for(Pair<OllamaTool, String> tool : tools)
+        {
+            Class<?> clazz = tool.getKey().getClass();
+            Field field = null;
+            while(!clazz.equals(Object.class)) {
+                try {
+                    field = clazz.getDeclaredField("source");
+                    if (field != null) {
+                        break;
+                    }
+                }
+                catch (NoSuchFieldException ignore){}
+                clazz = clazz.getSuperclass();
+            }
+            if (field != null) {
+                field.setAccessible(true);
+                try {
+                    field.set(tool.getKey(), tool.getValue());
+                } catch (IllegalAccessException e) {
+                    Core.writeLog("ERROR: "+e.getMessage());
+                }
+            }
+        }
+
         this.tools = tools;
         this.format = format;
         this.options = options;
@@ -139,7 +165,7 @@ public class OllamaObject {
      */
     public void addTool(OllamaTool tool, @MagicConstant(valuesFromClass = Core.Source.class) String source) {
         // We inject the source into the tool's source field if it exists, This is to not cause issues with duplicate tools
-        Class<? extends Object> clazz = tool.getClass();
+        Class<?> clazz = tool.getClass();
         Field field = null;
         while(!clazz.equals(Object.class)) {
             try {
@@ -351,7 +377,7 @@ public class OllamaObject {
          * @return The {@link OllamaObjectBuilder}
          */
         public OllamaObjectBuilder addTool(OllamaTool tool) {
-            this.tools.add(new Pair<>(tool, Core.Source.EXTERNAL));
+            this.tools.add(new Pair<>(tool, Core.Source.CTP));
             return this;
         }
 
@@ -374,7 +400,7 @@ public class OllamaObject {
          */
         public OllamaObjectBuilder addToolsExternal(ArrayList<? extends OllamaTool> tools) {
             for (OllamaTool tool : tools) {
-                this.tools.add(new Pair<>(tool, Core.Source.EXTERNAL));
+                this.tools.add(new Pair<>(tool, Core.Source.CTP));
             }
             return this;
         }
@@ -400,7 +426,7 @@ public class OllamaObject {
          */
         public OllamaObjectBuilder addTools(OllamaTool... tools) {
             for(OllamaTool tool : tools) {
-                this.tools.add(new Pair<>(tool, Core.Source.EXTERNAL));
+                this.tools.add(new Pair<>(tool, Core.Source.CTP));
             }
             return this;
         }

Display/src/main/java/me/neurodock/display/Display.java

@@ -56,12 +56,12 @@ public class Display {
 
         core.enablePlugins(Core.PLUGIN_DIRECTORY);
 
-        core.addTool(new TimeTool(), Core.Source.INTERNAL);
+        core.addTool(new TimeTool(), Core.Source.CTP);
         // TODO: Well Docker failes when luanched.... Fuck
-        core.addTool(new PythonRunner(core), Core.Source.INTERNAL);
-        core.addTools(new MALAPITool().getOllamaTools());
-        core.addTools(new GeniusTools().getGeniusTools());
-        core.addTools(new WikipediaTool().getWikipediaToolsInstance());
+        core.addTool(new PythonRunner(core), Core.Source.CTP);
+        //core.addTools(new MALAPITool().getOllamaTools());
+        //core.addTools(new GeniusTools().getGeniusTools());
+        //core.addTools(new WikipediaTool().getWikipediaToolsInstance());
 
         //APIApplication.start();
 

GeniusAPI/src/main/java/me/neurodock/genius/GeniusTools.java

@@ -73,7 +73,7 @@ public class GeniusTools {
                 if (OllamaFunctionTool.class.isAssignableFrom(clazz)) {
                     //System.out.println("Found endpoint: " + clazz.getName() + " With constructor: " + clazz.getDeclaredConstructors().f.getName() + " and arguments: " + Arrays.toString(clazz.getDeclaredConstructor().getParameterTypes()));
                     GeniusEndpointTool tool = (GeniusEndpointTool) clazz.getDeclaredConstructor(GeniusTools.class).newInstance(this);
-                    builder.addTool(tool, Core.Source.INTERNAL);
+                    builder.addTool(tool, Core.Source.CTP);
                 }
             }
         } catch (InvocationTargetException | InstantiationException | IllegalAccessException | NoSuchMethodException e) {

MALAPITool/src/main/java/me/neurodock/mal/api/MALAPITool.java

@@ -46,7 +46,7 @@ public class MALAPITool {
                 if (OllamaFunctionTool.class.isAssignableFrom(clazz)) {
                     //System.out.println("Found endpoint: " + clazz.getName() + " With constructor: " + clazz.getDeclaredConstructors().f.getName() + " and arguments: " + Arrays.toString(clazz.getDeclaredConstructor().getParameterTypes()));
                     MALEndpointTool tool = (MALEndpointTool) clazz.getDeclaredConstructor(MALAPITool.class).newInstance(MALAPITool.this);
-                    builder.addTool(tool, Core.Source.INTERNAL);
+                    builder.addTool(tool, Core.Source.CTP);
                 }
             }
         } catch (InvocationTargetException | InstantiationException | IllegalAccessException | NoSuchMethodException e) {

WikipediaTool/src/main/java/me/neurodock/wikipedia/WikipediaTool.java

@@ -13,7 +13,7 @@ public class WikipediaTool {
 
     public WikipediaTool() {
         this.wikipediaToolsInstance = OllamaFunctionTools.builder()
-                .addTool(new GetWikiPageText(), Core.Source.INTERNAL)
+                .addTool(new GetWikiPageText(), Core.Source.CTP)
                 .build();
     }