From ef6d6d534dab633168a02101c7e117983cdb1eeb Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Tue, 1 Jul 2025 18:26:06 +0200
Subject: [PATCH 01/13] fix: minor text clarifications in review panel

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 src/components/ReviewPanel.tsx | 103 ++++++++++++++++++---------------
 1 file changed, 55 insertions(+), 48 deletions(-)

diff --git a/src/components/ReviewPanel.tsx b/src/components/ReviewPanel.tsx
index ef5b8c9..a10d1ca 100644
--- a/src/components/ReviewPanel.tsx
+++ b/src/components/ReviewPanel.tsx
@@ -14,7 +14,7 @@ import {
   ChevronsDown,
   ChevronsUp,
   ChevronUp,
-  DraftingCompass,
+  Pen,
   GitCompare,
   Wrench,
   X,
@@ -365,9 +365,14 @@ const FileOperationItem = React.forwardRef<
             <button
               className="px-3 py-1 bg-red-500 dark:bg-red-600 text-white rounded hover:bg-red-600 dark:hover:bg-red-700 disabled:bg-gray-300 dark:disabled:bg-gray-600 disabled:cursor-not-allowed"
               disabled={op.accepted || op.rejected}
-            	onClick={() => onReject(index)}
+              onClick={() => onReject(index)}
+              title={
+                mode === 'git'
+                  ? 'Revert change to the last commit'
+                  : 'Reject change'
+              }
             >
-            	{mode === 'git' ? 'Revert Change' : 'Reject'}
+              {mode === 'git' ? 'Revert Change' : 'Reject'}
             </button>
           </div>
 
@@ -421,7 +426,7 @@ const ReviewPanel: React.FC = () => {
   // Handle clear operations with confirmation for AI mode
   const handleClear = () => {
     const { addLog } = useLogStore.getState();
-    
+
     if (mode === 'git') {
       // Git mode: clear immediately, no confirmation needed
       clearOperations();
@@ -434,11 +439,11 @@ const ReviewPanel: React.FC = () => {
       const pendingCount = activeOperations.filter(
         (op) => !op.accepted && !op.rejected
       ).length;
-      
+
       const confirmed = window.confirm(
         `There are ${pendingCount} pending change${pendingCount === 1 ? '' : 's'} that haven't been accepted or rejected.\n\nAre you sure you want to clear all changes? This action cannot be undone.`
       );
-      
+
       if (!confirmed) {
         return;
       }
@@ -1013,24 +1018,24 @@ const ReviewPanel: React.FC = () => {
               <Bot
                 size={18}
                 className="text-gray-500 dark:text-gray-400 flex-shrink-0 mt-0.5"
-            	/>
-            	<span>
-            		<strong>AI changes</strong> appear here after you use the "Apply AI
-            		Output" action. This processes responses from prompts like Coder{' '}
-            		<Wrench size={16} className="inline-block -mt-0.5" /> or Architect{' '}
-            		<DraftingCompass size={16} className="inline-block -mt-0.5" />.
-            	</span>
+              />
+              <span>
+                <strong>AI changes</strong> appear here after you use the "Apply
+                AI Output" action. This processes responses from prompts like
+                Coder <Wrench size={16} className="inline-block -mt-0.5" /> or
+                Writer <Pen size={16} className="inline-block -mt-0.5" />.
+              </span>
             </p>
             <p className="flex items-start gap-2">
-            	<GitCompare
-            		size={18}
-            		className="text-gray-500 dark:text-gray-400 flex-shrink-0 mt-0.5"
-            	/>
-            	<span>
-            		For <strong>Git changes</strong>, click the{' '}
-            		<GitCompare size={16} className="inline-block -mt-0.5" /> button
-            		above the file explorer.
-            	</span>
+              <GitCompare
+                size={18}
+                className="text-gray-500 dark:text-gray-400 flex-shrink-0 mt-0.5"
+              />
+              <span>
+                For <strong>Git changes</strong>, click the{' '}
+                <GitCompare size={16} className="inline-block -mt-0.5" /> button
+                above the file explorer.
+              </span>
             </p>
           </div>
         </div>
@@ -1106,30 +1111,32 @@ const ReviewPanel: React.FC = () => {
             <ChevronRight size={16} />
           </button>
           {mode === 'ai' && (
-          	<button
-          	  onClick={applyAllChanges}
-          	  disabled={!hasPendingOperations}
-          	  title={
-          	    hasPendingOperations
-          	      ? 'Accept all pending changes'
-          	      : 'No pending changes to accept'
-          	  }
-          	  className="ml-auto px-3 py-1 bg-green-500 dark:bg-green-600 text-white rounded hover:bg-green-600 dark:hover:bg-green-700 disabled:opacity-50 disabled:cursor-not-allowed"
-          	>
-          	  Accept All
-          	</button>
+            <button
+              onClick={applyAllChanges}
+              disabled={!hasPendingOperations}
+              title={
+                hasPendingOperations
+                  ? 'Accept all pending changes'
+                  : 'No pending changes to accept'
+              }
+              className="ml-auto px-3 py-1 bg-green-500 dark:bg-green-600 text-white rounded hover:bg-green-600 dark:hover:bg-green-700 disabled:opacity-50 disabled:cursor-not-allowed"
+            >
+              Accept All
+            </button>
           )}
           <button
-          	onClick={rejectAllChanges}
-          	disabled={!hasPendingOperations}
-          	title={
-          	  hasPendingOperations
-          	    ? 'Reject all pending changes'
-          	    : 'No pending changes to reject'
-          	}
-          	className={`${mode === 'ai' ? 'ml-2' : 'ml-auto'} px-3 py-1 bg-red-500 dark:bg-red-600 text-white rounded hover:bg-red-600 dark:hover:bg-red-700 disabled:opacity-50 disabled:cursor-not-allowed`}
+            onClick={rejectAllChanges}
+            disabled={!hasPendingOperations}
+            title={
+              mode === 'git'
+                ? 'Revert all changes to the last commit'
+                : hasPendingOperations
+                  ? 'Reject all pending changes'
+                  : 'No pending changes to reject'
+            }
+            className={`${mode === 'ai' ? 'ml-2' : 'ml-auto'} px-3 py-1 bg-red-500 dark:bg-red-600 text-white rounded hover:bg-red-600 dark:hover:bg-red-700 disabled:opacity-50 disabled:cursor-not-allowed`}
           >
-          	{mode === 'git' ? 'Revert All' : 'Reject All'}
+            {mode === 'git' ? 'Revert All' : 'Reject All'}
           </button>
           <button
             onClick={handleClear}
@@ -1137,7 +1144,7 @@ const ReviewPanel: React.FC = () => {
             title={
               activeOperations.length === 0
                 ? 'No changes to clear'
-                : mode === 'git' 
+                : mode === 'git'
                   ? 'Clear all changes'
                   : hasPendingOperations
                     ? 'Clear all changes (confirmation required)'
@@ -1178,14 +1185,14 @@ const ReviewPanel: React.FC = () => {
             <FileOperationItem
               key={`${op.file_path}-${idx}`}
               ref={(el) => {
-            	  itemRefs.current[idx] = el;
+                itemRefs.current[idx] = el;
               }}
               operation={op}
               index={idx}
               mode={mode}
-            	onAccept={applyChange}
-            	onReject={rejectChange}
-            	isActive={idx === currentIdx}
+              onAccept={applyChange}
+              onReject={rejectChange}
+              isActive={idx === currentIdx}
               onDiffBlocksCalculated={(blocks) => {
                 if (idx === currentIdx) {
                   setCurrentDiffBlocks(blocks);

From 87ba6e37ae7fe8f2fe21e085c0286542e14546f6 Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 08:46:54 +0200
Subject: [PATCH 02/13] fix: added ELECTRON_USE_DESKTOP_GL flag

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 docs/TROUBLESHOOTING.md | 28 +++++++++++++++++++++++++---
 electron/main.ts        | 13 +++++++++++++
 2 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/docs/TROUBLESHOOTING.md b/docs/TROUBLESHOOTING.md
index 46e9bce..0b48736 100644
--- a/docs/TROUBLESHOOTING.md
+++ b/docs/TROUBLESHOOTING.md
@@ -70,10 +70,32 @@ If you're running Athanor in WSL, installing `libsecret` alone is not sufficient
 
 </details>
 
----
-
-**IMPORTANT FINAL STEP (ALL DISTRIBUTIONS):**
+#### **IMPORTANT FINAL STEP (ALL DISTRIBUTIONS):**
 
 After the installation is complete, **you must log out and log back in**, or simply restart your computer. This ensures the newly installed keyring service is active and available to all applications, including Athanor.
 
 After restarting, when you first try to save a key, your system might prompt you to create a new default keyring and set a password for it. This is a one-time setup. Once completed, Athanor will be able to store API keys securely.
+
+---
+
+## Linux/WSL Graphics Issue (Blank Screen)
+
+### Problem: The application window is blank or black on startup
+
+When launching Athanor on certain Linux desktop environments or within the Windows Subsystem for Linux (WSL), the application may start, but the window remains completely blank. You may see a black or white screen instead of the user interface.
+
+### Cause
+
+This issue typically occurs when Electron, the framework used by Athanor, fails to automatically select the correct graphics rendering backend for your system. The default choice may be incompatible with your graphics driver setup, especially within the virtualized environment of WSL.
+
+### Solution
+
+You can resolve this by instructing Athanor to use a specific, more compatible graphics backend called "Desktop OpenGL." This is done by setting an environment variable before launching the application.
+
+1.  Open your shell's configuration file. This is usually `~/.bashrc`, `~/.zshrc`, or `~/.profile`, depending on your shell.
+2.  Add the following line to the end of the file:
+    ```bash
+    export ELECTRON_USE_DESKTOP_GL=1
+    ```
+3.  Save the file and restart your terminal, or run `source ~/.bashrc` (or the equivalent for your shell) to apply the changes.
+4.  Launch Athanor from the terminal. It should now start correctly with the UI visible.
diff --git a/electron/main.ts b/electron/main.ts
index 3f6495f..ba1507b 100644
--- a/electron/main.ts
+++ b/electron/main.ts
@@ -23,6 +23,19 @@ import {
 import { PROJECT_ANALYSIS } from '../src/utils/constants';
 import type { ApplicationSettings } from '../src/types/global';
 
+// --- WSL Graphics Fix Start ---
+// This addresses a specific rendering issue on WSL where Electron may default
+// to an incompatible graphics backend, causing a blank screen.
+// By checking for a custom environment variable, we allow affected users to opt-in
+// to forcing the 'desktop' OpenGL backend without affecting other users.
+if (process.env.ELECTRON_USE_DESKTOP_GL === '1') {
+  console.log(
+    '[Main] ELECTRON_USE_DESKTOP_GL=1 detected. Applying --use-gl=desktop switch.'
+  );
+  app.commandLine.appendSwitch('use-gl', 'desktop');
+}
+// --- WSL Graphics Fix End ---
+
 // Debug flag for menu diagnostics
 const DEBUG_MENU = false;
 const DEBUG_PATH = false;

From 4e2027a7959c297f2143c6ddcbe292a40f9d8fa0 Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 09:14:22 +0200
Subject: [PATCH 03/13] feat: accept CREATE if file already exists but add
 clear warning; feat: updated agentic architect prompt; chore: bumped version
 to 0.7.8

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 package.json                              |  2 +-
 resources/prompts/prompt_architect.xml    | 78 +++++++++++++++--------
 src/commands/parser/applyChangesParser.ts | 19 ++++--
 src/components/ReviewPanel.tsx            |  7 ++
 src/types/global.d.ts                     |  1 +
 5 files changed, 74 insertions(+), 33 deletions(-)

diff --git a/package.json b/package.json
index 56ef356..cec0d58 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "athanor",
-  "version": "0.7.7",
+  "version": "0.7.8",
   "bugs": {
     "url": "https://github.com/lacerbi/athanor/issues"
   },
diff --git a/resources/prompts/prompt_architect.xml b/resources/prompts/prompt_architect.xml
index 6433d15..50fafbf 100644
--- a/resources/prompts/prompt_architect.xml
+++ b/resources/prompts/prompt_architect.xml
@@ -479,36 +479,55 @@ The purpose is to:
 - All verification steps must be executable from the command line
 - Consider that the agent needs precise, unambiguous instructions
 
-The XML block should include:
+The XML block should be formatted as follows:
 
-1. An XML tag <ath command="task"></ath>
-  * The task_description slightly edited and rewritten for clarity (do not omit parts)
-  * An extended, thorough answer and analysis
-  * A high-level overview of the implementation strategy
-  * Break down the implementation into logical commits if the task is complex
-    - Each commit should focus on one self-contained piece of functionality
-    - Each commit should result in working (though potentially incomplete) code
-    - Each commit should modify a reasonable number of files (typically 1-3)
-    - Each commit should have a clear, specific purpose
-  * For each commit, provide:
-    - A clear description of what the commit achieves
-    - Files that will be modified
-    - Detailed step-by-step implementation instructions
-    - Any dependencies on previous commits
-    - **CLI-based verification commands** appropriate for the programming language and task
-  * For a simple task, one commit might be enough
+```xml
+<ath command="apply changes">
+<file>
+<file_message>Create new task file</file_message>
+<file_operation>CREATE</file_operation>
+<file_path>.ath_materials/TASK.md</file_path>
+<file_code><![CDATA[
+[Full Plan here]
+]]></file_code>
+</file>
+</ath>
+```
 
-2. A XML tag <ath command="select"></ath> with a list of all relevant files 
-  * List all the files that the developer will need to read in full, change or delete from the file_tree provided above
-  * Consider broadly which files might be useful to see for the feature, even if not immediately related
-  * These might include preloaders, utility or global constant files, etc.
-  * If in doubt whether you need to include a file, include it
-  * This list may match the list of highlighted (*) files above (if any), but might include additional files, or remove some which are clearly not needed
-  * Use the relative path of each file
+The full plan will contain:
+* The task_description slightly edited and rewritten for clarity (do not omit parts)
+* An extended, thorough answer and analysis
+* A high-level overview of the implementation strategy
+* Break down the implementation into logical commits if the task is complex
+  - Each commit should focus on one self-contained piece of functionality
+  - Each commit should result in working (though potentially incomplete) code
+  - Each commit should modify a reasonable number of files (typically 1-3)
+  - Each commit should have a clear, specific purpose
+* For each commit, provide:
+  - A clear description of what the commit achieves
+  - Files that will be modified
+  - Detailed step-by-step implementation instructions
+  - Any dependencies on previous commits
+  - **CLI-based verification commands** appropriate for the programming language and task
+* For a simple task, one commit might be enough
+
+At the end of the full plan, list "Relevant Files":
+
+* List all the files that the developer will need to read in full, change or delete from the file_tree provided above
+* Consider broadly which files might be useful to see for the feature, even if not immediately related
+* These might include preloaders, utility or global constant files, etc.
+* If in doubt whether you need to include a file, include it
+* This list may match the list of highlighted (*) files above (if any), but might include additional files, or remove some which are clearly not needed
+* Use the relative path of each file
 
 <example>
 ```xml
-<ath command="task">
+<ath command="apply changes">
+<file>
+<file_message>Create new task file</file_message>
+<file_operation>CREATE</file_operation>
+<file_path>.ath_materials/TASK.md</file_path>
+<file_code><![CDATA[
 # Task
 [Task description, rewritten for clarity]
 
@@ -548,10 +567,13 @@ The XML block should include:
   - API endpoints respond (if applicable)
 
 [Additional commits as needed...]
-</ath>
 
-<ath command="select">
-file1 file2 [...]
+# Relevant Files
+file1
+file2
+...
+]]></file_code>
+</file>
 </ath>
 ```
 </example>
diff --git a/src/commands/parser/applyChangesParser.ts b/src/commands/parser/applyChangesParser.ts
index c8e69a3..00629f7 100644
--- a/src/commands/parser/applyChangesParser.ts
+++ b/src/commands/parser/applyChangesParser.ts
@@ -265,8 +265,18 @@ export async function parseXmlContent(
       try {
         let oldCode = '';
         let processedNewCode = '';
-        const operation = block.operation;
+        let operation = block.operation;
         const path = block.path;
+        let warning: string | undefined;
+
+        if (operation === 'CREATE') {
+          const fileExists = await window.fileService.exists(path);
+          if (fileExists) {
+            operation = 'UPDATE_FULL';
+            warning = `File already exists. Operation changed from CREATE to a full update.`;
+            addLog(`Warning for ${path}: ${warning}`);
+          }
+        }
 
         // Track failed UPDATE_DIFF operations
         if (operation === 'UPDATE_DIFF') {
@@ -276,9 +286,9 @@ export async function parseXmlContent(
         // Get existing file content if needed
         if (operation !== 'CREATE') {
           try {
-            const isDir = await window.fileSystem.isDirectory(path);
+            const isDir = await window.fileService.isDirectory(path);
             if (!isDir) {
-              oldCode = (await window.fileSystem.readFile(path, {
+              oldCode = (await window.fileService.read(path, {
                 encoding: 'utf8',
               })) as string;
             } else {
@@ -329,6 +339,7 @@ export async function parseXmlContent(
           accepted: false,
           rejected: false,
           diff_blocks: operation === 'UPDATE_DIFF' ? [] : undefined,
+          warning: warning,
         });
       } catch (error) {
         console.error(`Error processing file ${block.path}:`, error);
@@ -338,7 +349,7 @@ export async function parseXmlContent(
 
     // If there were any failed UPDATE_DIFF operations, create a clickable log entry
     if (failedDiffPaths.length > 0) {
-      const currentDir = await window.fileSystem.getCurrentDirectory();
+      const currentDir = await window.fileService.getCurrentDirectory();
       // Create a clickable log entry by passing an object
       addLog({
         message: `${failedDiffPaths.length} UPDATE_DIFF operation(s) failed - Click to copy files`,
diff --git a/src/components/ReviewPanel.tsx b/src/components/ReviewPanel.tsx
index a10d1ca..6aa16c0 100644
--- a/src/components/ReviewPanel.tsx
+++ b/src/components/ReviewPanel.tsx
@@ -341,6 +341,13 @@ const FileOperationItem = React.forwardRef<
           </div>
         </div>
 
+        {op.warning && (
+          <div className="flex items-start gap-2 p-3 my-2 text-sm rounded-md bg-amber-100 dark:bg-amber-900/30 text-amber-800 dark:text-amber-200 border border-amber-200 dark:border-amber-800">
+            <AlertTriangle className="w-4 h-4 mt-0.5 flex-shrink-0" />
+            <p>{op.warning}</p>
+          </div>
+        )}
+
         <div className="min-w-0 w-full">
           <DiffView
             oldText={op.old_code}
diff --git a/src/types/global.d.ts b/src/types/global.d.ts
index 567c023..65213b8 100644
--- a/src/types/global.d.ts
+++ b/src/types/global.d.ts
@@ -638,4 +638,5 @@ export interface FileOperation {
   accepted: boolean;
   rejected: boolean;
   diff_blocks?: DiffBlock[]; // Only used for UPDATE_DIFF operations
+  warning?: string;
 }

From a69b80cab3dbf26e01ed08e0c87b31edcde62186 Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 11:51:06 +0200
Subject: [PATCH 04/13] feat: added agent task command

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 resources/prompts/prompt_architect.xml | 24 ++++++----------
 src/actions/ApplyAiOutputAction.ts     |  7 +++++
 src/commands/agentTaskCommand.ts       | 40 ++++++++++++++++++++++++++
 src/commands/index.ts                  |  2 ++
 src/commands/types.ts                  |  3 +-
 5 files changed, 59 insertions(+), 17 deletions(-)
 create mode 100644 src/commands/agentTaskCommand.ts

diff --git a/resources/prompts/prompt_architect.xml b/resources/prompts/prompt_architect.xml
index 50fafbf..a059bb2 100644
--- a/resources/prompts/prompt_architect.xml
+++ b/resources/prompts/prompt_architect.xml
@@ -482,15 +482,11 @@ The purpose is to:
 The XML block should be formatted as follows:
 
 ```xml
-<ath command="apply changes">
-<file>
-<file_message>Create new task file</file_message>
-<file_operation>CREATE</file_operation>
-<file_path>.ath_materials/TASK.md</file_path>
-<file_code><![CDATA[
+<ath command="agent task">
+<file_name>TASK.md</file_name>
+<task_content>
 [Full Plan here]
-]]></file_code>
-</file>
+</file_content>
 </ath>
 ```
 
@@ -522,12 +518,9 @@ At the end of the full plan, list "Relevant Files":
 
 <example>
 ```xml
-<ath command="apply changes">
-<file>
-<file_message>Create new task file</file_message>
-<file_operation>CREATE</file_operation>
-<file_path>.ath_materials/TASK.md</file_path>
-<file_code><![CDATA[
+<ath command="agent task">
+<file_name>TASK.md</file_name>
+<task_content>
 # Task
 [Task description, rewritten for clarity]
 
@@ -572,8 +565,7 @@ At the end of the full plan, list "Relevant Files":
 file1
 file2
 ...
-]]></file_code>
-</file>
+</task_content>
 </ath>
 ```
 </example>
diff --git a/src/actions/ApplyAiOutputAction.ts b/src/actions/ApplyAiOutputAction.ts
index 4f481d9..4a57fad 100644
--- a/src/actions/ApplyAiOutputAction.ts
+++ b/src/actions/ApplyAiOutputAction.ts
@@ -81,6 +81,13 @@ export async function processAiResponseContent(
           });
           break;
 
+        case commands.COMMAND_TYPES.AGENT_TASK:
+          success = await commands.executeAgentTaskCommand({
+            content: command.content,
+            addLog,
+          });
+          break;
+
         default:
           addLog(`Unknown command type: ${command.type}`);
           continue;
diff --git a/src/commands/agentTaskCommand.ts b/src/commands/agentTaskCommand.ts
new file mode 100644
index 0000000..2d72bb2
--- /dev/null
+++ b/src/commands/agentTaskCommand.ts
@@ -0,0 +1,40 @@
+import { extractTagContent } from '../utils/extractTagContent';
+
+export interface AgentTaskCommandParams {
+  content: string;
+  addLog: (message: string) => void;
+}
+
+export async function executeAgentTaskCommand({
+  content,
+  addLog,
+}: AgentTaskCommandParams): Promise<boolean> {
+  try {
+    const fileName = extractTagContent(content, 'file_name');
+    const taskContent = extractTagContent(content, 'task_content');
+
+    if (!fileName) {
+      addLog('Error: "agent task" command is missing <file_name>.');
+      return false;
+    }
+
+    if (!taskContent) {
+      addLog('Error: "agent task" command is missing <task_content>.');
+      return false;
+    }
+
+    const materialsDir = await window.fileService.getMaterialsDir();
+    const filePath = await window.pathUtils.join(materialsDir, fileName);
+    const displayPath = await window.pathUtils.relative(filePath);
+
+    await window.fileService.write(filePath, taskContent);
+
+    addLog(`Successfully wrote agent task to: ${displayPath}`);
+    return true;
+  } catch (error) {
+    const errorMessage = error instanceof Error ? error.message : String(error);
+    addLog(`Error executing "agent task" command: ${errorMessage}`);
+    console.error('Agent Task execution failed:', error);
+    return false;
+  }
+}
diff --git a/src/commands/index.ts b/src/commands/index.ts
index 40ed837..f4e210c 100644
--- a/src/commands/index.ts
+++ b/src/commands/index.ts
@@ -5,9 +5,11 @@
 export { executeSelectCommand } from './selectCommand';
 export { executeTaskCommand } from './taskCommand';
 export { executeApplyChangesCommand } from './applyChangesCommand';
+export { executeAgentTaskCommand } from './agentTaskCommand';
 export type { SelectCommandParams } from './selectCommand';
 export type { TaskCommandParams } from './taskCommand';
 export type { ApplyChangesParams } from './applyChangesCommand';
+export type { AgentTaskCommandParams } from './agentTaskCommand';
 
 // Command types and constants
 export { COMMAND_TYPES } from './types';
diff --git a/src/commands/types.ts b/src/commands/types.ts
index 122440a..bde4296 100644
--- a/src/commands/types.ts
+++ b/src/commands/types.ts
@@ -6,9 +6,10 @@ export const COMMAND_TYPES = {
   SELECT: 'select',
   TASK: 'task',
   APPLY_CHANGES: 'apply changes',
+  AGENT_TASK: 'agent task',
 } as const;
 
-export type CommandType = typeof COMMAND_TYPES[keyof typeof COMMAND_TYPES];
+export type CommandType = (typeof COMMAND_TYPES)[keyof typeof COMMAND_TYPES];
 
 // Re-export common types used across commands
 export type { FileOperation } from '../types/global';

From 94aa97fea2a23388a655c7c0d5bb045c52f9223b Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 13:08:40 +0200
Subject: [PATCH 05/13] feat: add task name to agent prompt

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 resources/prompts/prompt_architect.xml |  6 ++++--
 src/actions/buildTaskAction.ts         |  1 +
 src/components/ActionPanel.tsx         |  1 +
 src/utils/buildPrompt.ts               | 11 ++++++++++-
 4 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/resources/prompts/prompt_architect.xml b/resources/prompts/prompt_architect.xml
index a059bb2..c551903 100644
--- a/resources/prompts/prompt_architect.xml
+++ b/resources/prompts/prompt_architect.xml
@@ -483,13 +483,15 @@ The XML block should be formatted as follows:
 
 ```xml
 <ath command="agent task">
-<file_name>TASK.md</file_name>
+<file_name>{{task_tab_name}}.md</file_name>
 <task_content>
 [Full Plan here]
 </file_content>
 </ath>
 ```
 
+Use the provided task file name `{{task_tab_name}}.md`
+
 The full plan will contain:
 * The task_description slightly edited and rewritten for clarity (do not omit parts)
 * An extended, thorough answer and analysis
@@ -519,7 +521,7 @@ At the end of the full plan, list "Relevant Files":
 <example>
 ```xml
 <ath command="agent task">
-<file_name>TASK.md</file_name>
+<file_name>{{task_tab_name}}.md</file_name>
 <task_content>
 # Task
 [Task description, rewritten for clarity]
diff --git a/src/actions/buildTaskAction.ts b/src/actions/buildTaskAction.ts
index 777b9da..1965994 100644
--- a/src/actions/buildTaskAction.ts
+++ b/src/actions/buildTaskAction.ts
@@ -71,6 +71,7 @@ export async function buildTaskAction(params: BuildTaskActionParams): Promise<vo
       currentDir,
       activeTab.content,
       activeTab.context,
+      activeTab.name,
       undefined, // passedFormatTypeOverride
       undefined, // smartPreviewConfigInput
       currentThresholdLineLength
diff --git a/src/components/ActionPanel.tsx b/src/components/ActionPanel.tsx
index 0359fd9..7b13cd6 100644
--- a/src/components/ActionPanel.tsx
+++ b/src/components/ActionPanel.tsx
@@ -229,6 +229,7 @@ const ActionPanel: React.FC<ActionPanelProps> = ({
         await window.fileSystem.getCurrentDirectory(),
         tabs[activeTabIndex].content, // Current tab's content
         tabs[activeTabIndex].context, // Current tab's context
+        activeTab.name, // Pass the active tab's name
         formatType, // Pass the current format type
         smartPreviewConfig, // Pass the smart preview configuration from settings
         currentThresholdLineLength // Pass the current threshold line length
diff --git a/src/utils/buildPrompt.ts b/src/utils/buildPrompt.ts
index 4ab9681..5b03f20 100644
--- a/src/utils/buildPrompt.ts
+++ b/src/utils/buildPrompt.ts
@@ -23,6 +23,7 @@ export interface PromptVariables {
   selected_files?: string;
   selected_files_with_info?: string;
   task_context?: string;
+  task_tab_name?: string;
   threshold_line_length?: number;
   include_ai_summaries?: boolean;
 }
@@ -92,9 +93,10 @@ export async function buildDynamicPrompt(
   rootPath: string,
   taskDescription: string = '',
   taskContext: string = '',
+  activeTabName: string,
   passedFormatTypeOverride?: string,
   smartPreviewConfigInput?: { minLines: number; maxLines: number },
-  currentThresholdLineLength?: number // Added new parameter
+  currentThresholdLineLength?: number
 ): Promise<string> {
   // Get the store settings and effective configuration
   const {
@@ -179,6 +181,12 @@ export async function buildDynamicPrompt(
     ? `\n<task_context>\n${taskContext.trim()}\n</task_context>`
     : '';
 
+  // Sanitize and format the tab name
+  const formattedTabName = (activeTabName || '')
+    .toUpperCase()
+    .replace(/\s+/g, '_') // Replace whitespace with underscores
+    .replace(/[^A-Z0-9_]/g, ''); // Remove any remaining non-alphanumeric characters except underscore
+
   // Create a copy of codebaseDoc to avoid modifying the original
   const codebaseContent = { ...codebaseDoc };
 
@@ -193,6 +201,7 @@ export async function buildDynamicPrompt(
     project_info: projectInfoForPrompt,
     task_description: taskDescription,
     task_context: formattedTaskContext,
+    task_tab_name: formattedTabName,
     selected_files: getSelectedFilesList(items, selectedFiles, rootPath),
     selected_files_with_info: getSelectedFilesWithInfo(
       items,

From 67ba73ee927c4987e2adc2c38ab0d99e6a937946 Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:04:49 +0200
Subject: [PATCH 06/13] feat: add clickable log for agent task command

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 src/commands/agentTaskCommand.ts | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/commands/agentTaskCommand.ts b/src/commands/agentTaskCommand.ts
index 2d72bb2..4a17d67 100644
--- a/src/commands/agentTaskCommand.ts
+++ b/src/commands/agentTaskCommand.ts
@@ -1,8 +1,14 @@
+// AI Summary: Command handler for creating agent tasks.
+// Parses file_name and task_content from an XML block, writes the content to a file in the .ath_materials directory,
+// and logs a clickable success message that copies an instruction to the clipboard.
 import { extractTagContent } from '../utils/extractTagContent';
+import { copyToClipboard } from '../actions';
 
 export interface AgentTaskCommandParams {
   content: string;
-  addLog: (message: string) => void;
+  addLog: (
+    message: string | { message: string; onClick: () => Promise<void> }
+  ) => void;
 }
 
 export async function executeAgentTaskCommand({
@@ -29,7 +35,17 @@ export async function executeAgentTaskCommand({
 
     await window.fileService.write(filePath, taskContent);
 
-    addLog(`Successfully wrote agent task to: ${displayPath}`);
+    const instruction = `Review and execute the instructions in ${displayPath}`;
+    addLog({
+      message: `Agent task created: ${displayPath}. Click to copy instruction.`,
+      onClick: async () => {
+        await copyToClipboard({
+          content: instruction,
+          addLog: (msg: string) => addLog(msg),
+        });
+      },
+    });
+
     return true;
   } catch (error) {
     const errorMessage = error instanceof Error ? error.message : String(error);

From 7743aa813a4d9cab8caff323fd2b99b540e1723f Mon Sep 17 00:00:00 2001
From: lacerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:08:06 +0200
Subject: [PATCH 07/13] feat: added listened for ctrl C ctrl V

Signed-off-by: lacerbi <luigi.acerbi@gmail.com>
---
 package-lock.json           |  4 ++--
 src/components/CliPanel.tsx | 25 +++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 1ac651d..e843c12 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "athanor",
-  "version": "0.7.5",
+  "version": "0.7.7",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "athanor",
-      "version": "0.7.5",
+      "version": "0.7.7",
       "license": "Apache-2.0",
       "dependencies": {
         "@anthropic-ai/sdk": "^0.52.0",
diff --git a/src/components/CliPanel.tsx b/src/components/CliPanel.tsx
index e06eb89..36c0fe4 100644
--- a/src/components/CliPanel.tsx
+++ b/src/components/CliPanel.tsx
@@ -28,6 +28,31 @@ const CliPanel: React.FC<CliPanelProps> = ({ currentDirectory, isVisible }) => {
     termInstanceRef.current = { term, fitAddon };
     term.open(terminalRef.current);
 
+    // Add custom key event handler for copy/paste
+    term.attachCustomKeyEventHandler((event) => {
+      // Handle Ctrl+C (copy)
+      if (event.ctrlKey && event.key === 'c' && term.hasSelection()) {
+        navigator.clipboard.writeText(term.getSelection());
+        return false; // Prevent default terminal behavior
+      }
+      // Handle Ctrl+V (paste)
+      if (event.ctrlKey && event.key === 'v') {
+        navigator.clipboard.readText().then((text) => {
+          if (text) {
+            // Send the pasted text to the terminal
+            const sessionId = useCliStore
+              .getState()
+              .getSessionId(currentDirectory);
+            if (sessionId) {
+              window.electronBridge.shell.write(sessionId, text);
+            }
+          }
+        });
+        return false; // Prevent default terminal behavior
+      }
+      return true; // Let other keys pass through
+    });
+
     (async () => {
       let sessionId = useCliStore.getState().getSessionId(currentDirectory);
       if (!sessionId) {

From 8050594177c6a56164e1e154f8494c5c7d4b6fb8 Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:10:05 +0200
Subject: [PATCH 08/13] test: fixed tests after addition of new command

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 src/actions/buildTaskAction.test.ts | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/actions/buildTaskAction.test.ts b/src/actions/buildTaskAction.test.ts
index 0a63f4b..e4b5443 100644
--- a/src/actions/buildTaskAction.test.ts
+++ b/src/actions/buildTaskAction.test.ts
@@ -241,6 +241,7 @@ describe('buildTaskAction', () => {
         '/fake/project/dir',
         'existing task description',
         'existing context',
+        'Task 1', // activeTabName
         undefined, // passedFormatTypeOverride
         undefined, // smartPreviewConfigInput
         200 // currentThresholdLineLength
@@ -284,6 +285,7 @@ describe('buildTaskAction', () => {
         expect.anything(),
         expect.anything(),
         expect.anything(),
+        'Task 1',
         undefined,
         undefined,
         150 // should use the passed value
@@ -398,6 +400,7 @@ describe('buildTaskAction', () => {
         expect.anything(),
         'existing task description', // from mocked store state
         'existing context', // from mocked store state
+        'Task 1',
         undefined,
         undefined,
         expect.anything()
@@ -442,6 +445,7 @@ describe('buildTaskAction', () => {
         expect.anything(),
         expect.anything(),
         expect.anything(),
+        'Task 1',
         undefined,
         undefined,
         expect.anything()
@@ -492,6 +496,7 @@ describe('buildTaskAction', () => {
         expect.anything(),
         expect.anything(),
         expect.anything(),
+        'Task 1',
         undefined,
         undefined,
         expect.anything()
@@ -515,6 +520,7 @@ describe('buildTaskAction', () => {
         expect.anything(),
         expect.anything(),
         expect.anything(),
+        'Task 1',
         undefined,
         undefined,
         expect.anything()

From bfb3a3ed9417280d2ba3ccb416a24fb130f447eb Mon Sep 17 00:00:00 2001
From: lacerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:33:59 +0200
Subject: [PATCH 09/13] fix: fixed paste behavior

Signed-off-by: lacerbi <luigi.acerbi@gmail.com>
---
 src/components/CliPanel.tsx | 54 +++++++++++++++++++++++++++++--------
 1 file changed, 43 insertions(+), 11 deletions(-)

diff --git a/src/components/CliPanel.tsx b/src/components/CliPanel.tsx
index 36c0fe4..d8795ca 100644
--- a/src/components/CliPanel.tsx
+++ b/src/components/CliPanel.tsx
@@ -16,6 +16,8 @@ const CliPanel: React.FC<CliPanelProps> = ({ currentDirectory, isVisible }) => {
     null
   );
   const listenersAttached = useRef(false);
+  const lastPasteTime = useRef(0);
+  const isPasting = useRef(false);
 
   // Effect to initialize the terminal once per project (due to key={currentDirectory})
   useEffect(() => {
@@ -35,19 +37,44 @@ const CliPanel: React.FC<CliPanelProps> = ({ currentDirectory, isVisible }) => {
         navigator.clipboard.writeText(term.getSelection());
         return false; // Prevent default terminal behavior
       }
-      // Handle Ctrl+V (paste)
+      // Handle Ctrl+V (paste) - only on keydown to prevent double execution
       if (event.ctrlKey && event.key === 'v') {
-        navigator.clipboard.readText().then((text) => {
-          if (text) {
-            // Send the pasted text to the terminal
-            const sessionId = useCliStore
-              .getState()
-              .getSessionId(currentDirectory);
-            if (sessionId) {
-              window.electronBridge.shell.write(sessionId, text);
+        if (event.type !== 'keydown') {
+          return false; // Ignore keyup events
+        }
+
+        event.preventDefault();
+        event.stopPropagation();
+
+        if (isPasting.current) {
+          console.log('[CliPanel] Already processing paste, ignoring');
+          return false;
+        }
+
+        isPasting.current = true;
+        console.log('[CliPanel] Processing paste event');
+
+        navigator.clipboard
+          .readText()
+          .then((text) => {
+            if (text) {
+              // Send the pasted text to the terminal
+              const sessionId = useCliStore
+                .getState()
+                .getSessionId(currentDirectory);
+              if (sessionId) {
+                window.electronBridge.shell.write(sessionId, text);
+              }
             }
-          }
-        });
+            // Reset the flag after a delay
+            setTimeout(() => {
+              isPasting.current = false;
+            }, 100);
+          })
+          .catch((err) => {
+            console.error('[CliPanel] Failed to read clipboard:', err);
+            isPasting.current = false;
+          });
         return false; // Prevent default terminal behavior
       }
       return true; // Let other keys pass through
@@ -68,6 +95,11 @@ const CliPanel: React.FC<CliPanelProps> = ({ currentDirectory, isVisible }) => {
 
       if (!listenersAttached.current) {
         term.onData((data) => {
+          // Skip if we're handling a paste operation
+          if (isPasting.current) {
+            console.log('[CliPanel] Skipping onData during paste operation');
+            return;
+          }
           window.electronBridge.shell.write(sessionId, data);
         });
         term.onResize(({ cols, rows }) => {

From c02b34a0481f1a63b0aa674b0330afe7a79cca2e Mon Sep 17 00:00:00 2001
From: lacerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:40:03 +0200
Subject: [PATCH 10/13] docs: updated linting situation (use prettier)

Signed-off-by: lacerbi <luigi.acerbi@gmail.com>
---
 CLAUDE.md  | 4 ++--
 PROJECT.md | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index eb24d33..f762636 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -14,7 +14,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 - `npm test` - Run Jest unit tests (includes both main and renderer process tests)
 - `npm run test:watch` - Run tests in watch mode
-- `npm run lint` - Run ESLint on TypeScript/React code
+- `npm run lint` - **Note: Currently non-functional** due to ESLint configuration incompatibility (`.eslintrc.js` uses old format incompatible with ESLint 9+). Prettier is used for code formatting.
 
 **Platform-specific builds:**
 
@@ -117,7 +117,7 @@ Athanor is an Electron desktop application for AI-assisted development workflows
 **Code style:**
 
 - TypeScript 5+ with strict typing
-- ESLint + Prettier configuration
+- Prettier for code formatting (ESLint config exists but is incompatible with ESLint 9+)
 - TailwindCSS 3 + Material-UI components
 - Conventional Commits for commit messages
 
diff --git a/PROJECT.md b/PROJECT.md
index 8d7d639..31d65e3 100644
--- a/PROJECT.md
+++ b/PROJECT.md
@@ -158,7 +158,8 @@ Athanor follows Electron's recommended **“secure by default”** pattern, sepa
 - **Webpack & electron-forge**: Build, package, and run the Electron application.
 - **TailwindCSS 3 + Lucide Icons**: Provides a flexible styling system and icon library for a clean UI.
 - **Material-UI (MUI) 5**: Partially integrated for certain UI elements (used in some components).
-- **ESLint / Prettier**: Linting & formatting for consistent code style.
+- **Prettier**: Code formatting for consistent style (configured via `.prettierrc`).
+- **ESLint**: Currently non-functional due to incompatible configuration format (`.eslintrc.js` uses old format incompatible with ESLint 9+). The `npm run lint` command will not work properly.
 - **Jest & ts-jest**: Provide the unit testing framework. Tests are typically colocated with the source code they validate (e.g., `FileService.test.ts` alongside `FileService.ts`).
 - **Testing Mocks**: Key dependencies, including Electron itself (via `tests/__mocks__/electron.ts`) and Node.js modules like `fs/promises`, are mocked to ensure isolated and reliable unit tests.
 

From fdc032da36bfafb2b8feab20b9f4da6a3bf3928d Mon Sep 17 00:00:00 2001
From: lacerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:47:31 +0200
Subject: [PATCH 11/13] docs: updated CLAUDE.md

Signed-off-by: lacerbi <luigi.acerbi@gmail.com>
---
 CLAUDE.md | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/CLAUDE.md b/CLAUDE.md
index f762636..ca5202c 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -39,6 +39,11 @@ Athanor is an Electron desktop application for AI-assisted development workflows
 - `RelevanceEngineService.ts` - Intelligent context discovery using multiple heuristics
 - `ProjectGraphService.ts` - Background project analysis and dependency mapping
 - `GitService.ts` - Git repository analysis for relevance scoring
+- `UserActivityService.ts` - Real-time file activity tracking for relevance signals
+- `SettingsService.ts` - Project and application settings management
+- `ShellService.ts` - Terminal/CLI session management with persistent PTY sessions
+- `TaskAnalysisUtils.ts` - Task description analysis and keyword extraction
+- `DependencyResolver.ts` / `DependencyScanner.ts` - Language-aware dependency analysis
 
 ### Critical File System Patterns
 
@@ -63,6 +68,10 @@ Athanor is an Electron desktop application for AI-assisted development workflows
 - `promptStore.ts` - Prompt templates and variants
 - `taskStore.ts` - Task templates and variants
 - `applyChangesStore.ts` - AI-generated file change management
+- `settingsStore.ts` - Project and application settings state
+- `logStore.ts` - Application log management with interactive entries
+- `commandStore.ts` - Clipboard and command validation state
+- `cliStore.ts` - Terminal session state management
 
 ### Project Structure Insights
 
@@ -71,18 +80,47 @@ Athanor is an Electron desktop application for AI-assisted development workflows
 - Relevance Engine uses Git history, dependencies, file mentions, and user activity
 - Project analysis runs in background worker thread (`projectAnalysisWorker.ts`)
 - Results cached in `.ath_materials/project_graph.json`
+- Two-phase scoring engine with multiple heuristics for relevance
+- Automatic re-analysis when file changes are detected after inactivity
 
 **AI Integration:**
 
 - Optional direct API integration via secure storage (`electron/modules/secure-api-storage/`)
 - Primary workflow: copy prompts to external AI, paste responses back
 - XML command parsing for applying AI-generated changes
+- Modular LLM provider system (`electron/modules/llm/`) supporting:
+  - Anthropic Claude API
+  - OpenAI GPT models
+  - Google Gemini models
+  - Mistral models (API key storage only)
+- Type-safe IPC channels for LLM operations
+- Extensive model configuration and client adapters
 
 **File Management:**
 
 - Supports `.athignore` and `.gitignore` patterns
 - Chokidar file watchers for real-time updates
 - Path normalization via `PathUtils.ts`
+- Agent task creation in `.ath_materials` directory
+
+**CLI/Terminal Support:**
+
+- Integrated terminal via `node-pty` and `xterm.js`
+- Multi-session support with persistent terminals
+- Platform-specific shell detection (PowerShell on Windows, zsh/bash on Unix)
+- Managed by `ShellService.ts` and `cliStore.ts`
+
+**Additional Features:**
+
+- **Tooltips**: Contextual help throughout the UI via hover tooltips
+- **Drag and Drop**: File paths can be dragged from explorer to task/context areas
+- **Context Suggestions**: Automatic context suggestions based on task content
+- **Preset Tasks**: Pre-defined task templates loaded from `task_*.xml` files
+- **Token Budgeting**: Intelligent file inclusion based on token limits
+- **Smart Preview**: Configurable preview of file contents in prompts
+- **Documentation Format**: Multiple format options for file inclusion
+- **Ignore Rules**: Advanced pattern matching with `.athignore` and `.gitignore`
+- **Project Settings**: Stored in `.ath_materials/project_settings.json`
 
 ## Testing Considerations
 
@@ -108,6 +146,22 @@ Athanor is an Electron desktop application for AI-assisted development workflows
 4. Update `src/types/global.d.ts` type definitions
 5. Implement UI-level operations in `fileSystemService.ts`
 
+**When adding new IPC handlers:**
+
+1. Create handler functions in appropriate file in `electron/handlers/`
+2. Export from `ipcHandlers.ts` for registration
+3. Add corresponding methods to `preload.ts`
+4. Update type definitions in `src/types/global.d.ts`
+
+**Important UI Patterns:**
+
+- **Left Panel**: File explorer with context menus and ignore functionality
+- **Right Panel**: Task tabs, file viewer, and Apply Changes panel
+- **Bottom Panel**: Log viewer with clickable entries for debugging
+- **Action Panel**: Controls for prompt generation, preset tasks, and settings toggles
+- **Task Templates**: XML-based templates in `resources/prompts/`
+- **Prompt Variants**: Context menu for switching between prompt modes (Query, Coder, Architect)
+
 **Security considerations:**
 
 - Never bypass IPC bridge for file operations
@@ -131,3 +185,8 @@ Athanor is an Electron desktop application for AI-assisted development workflows
 - **ignore** - .gitignore/.athignore parsing
 - **js-tiktoken** - Token counting for prompts
 - **Jest + ts-jest** - Testing framework
+- **@anthropic-ai/sdk** - Anthropic Claude API integration
+- **openai** - OpenAI API integration
+- **@google/genai** - Google Gemini API integration
+- **node-pty** - Terminal emulation support
+- **xterm & xterm-addon-fit** - Terminal rendering in UI

From b2f15cbcee71ba26dc226b2981c650f02c2a11fe Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:48:47 +0200
Subject: [PATCH 12/13] docs: added GEMINI.md - clone of CLAUDE.md

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 GEMINI.md | 192 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 192 insertions(+)
 create mode 100644 GEMINI.md

diff --git a/GEMINI.md b/GEMINI.md
new file mode 100644
index 0000000..a111b00
--- /dev/null
+++ b/GEMINI.md
@@ -0,0 +1,192 @@
+# GEMINI.md
+
+This file provides guidance to Gemini CLI when working with code in this repository.
+
+## Essential Commands
+
+**Development:**
+
+- `npm run package` - **(Standard)** Build a local production application (in `out/`). This is the recommended way to test changes.
+- `npm start` or `npm run dev` - **(Deprecated for testing)** Start development mode with hot reload. Do not use.
+- `npm run make` - Unsupported. Do not use.
+
+**Testing & Quality:**
+
+- `npm test` - Run Jest unit tests (includes both main and renderer process tests)
+- `npm run test:watch` - Run tests in watch mode
+- `npm run lint` - **Note: Currently non-functional** due to ESLint configuration incompatibility (`.eslintrc.js` uses old format incompatible with ESLint 9+). Prettier is used for code formatting.
+
+**Platform-specific builds:**
+
+- `npm run build:win` - Build for Windows
+- `npm run build:linux` - Build for Linux
+
+## Architecture Overview
+
+Athanor is an Electron desktop application for AI-assisted development workflows. It helps developers create context-rich prompts and apply AI-generated changes to codebases.
+
+### Core Architecture Principles
+
+**Main/Renderer Separation:**
+
+- **Main Process** (`electron/`): File system operations, Git integration, project analysis
+- **Renderer Process** (`src/`): React UI, state management with Zustand
+- **IPC Communication**: Secure bridge via `preload.ts` and typed in `src/types/global.d.ts`
+
+**Key Services:**
+
+- `FileService.ts` - Central file system operations manager (main process)
+- `RelevanceEngineService.ts` - Intelligent context discovery using multiple heuristics
+- `ProjectGraphService.ts` - Background project analysis and dependency mapping
+- `GitService.ts` - Git repository analysis for relevance scoring
+- `UserActivityService.ts` - Real-time file activity tracking for relevance signals
+- `SettingsService.ts` - Project and application settings management
+- `ShellService.ts` - Terminal/CLI session management with persistent PTY sessions
+- `TaskAnalysisUtils.ts` - Task description analysis and keyword extraction
+- `DependencyResolver.ts` / `DependencyScanner.ts` - Language-aware dependency analysis
+
+### Critical File System Patterns
+
+**Always use proper abstraction layers:**
+
+- Main process: Use `FileService.ts` singleton for all file operations
+- Renderer process: Use `fileSystemService.ts` for UI-related file operations
+- Never bypass IPC for file operations from renderer
+
+**Global type definitions:**
+
+- `src/types/global.d.ts` - Extends window interface and defines core types
+- Must be updated when modifying IPC method signatures
+
+### State Management
+
+**Zustand stores in `src/stores/`:**
+
+- `fileSystemStore.ts` - Selected files, file tree, preview state
+- `workbenchStore.ts` - Multi-tab task management
+- `contextStore.ts` - Intelligent context builder state
+- `promptStore.ts` - Prompt templates and variants
+- `taskStore.ts` - Task templates and variants
+- `applyChangesStore.ts` - AI-generated file change management
+- `settingsStore.ts` - Project and application settings state
+- `logStore.ts` - Application log management with interactive entries
+- `commandStore.ts` - Clipboard and command validation state
+- `cliStore.ts` - Terminal session state management
+
+### Project Structure Insights
+
+**Core Intelligence:**
+
+- Relevance Engine uses Git history, dependencies, file mentions, and user activity
+- Project analysis runs in background worker thread (`projectAnalysisWorker.ts`)
+- Results cached in `.ath_materials/project_graph.json`
+- Two-phase scoring engine with multiple heuristics for relevance
+- Automatic re-analysis when file changes are detected after inactivity
+
+**AI Integration:**
+
+- Optional direct API integration via secure storage (`electron/modules/secure-api-storage/`)
+- Primary workflow: copy prompts to external AI, paste responses back
+- XML command parsing for applying AI-generated changes
+- Modular LLM provider system (`electron/modules/llm/`) supporting:
+  - Anthropic Claude API
+  - OpenAI GPT models
+  - Google Gemini models
+  - Mistral models (API key storage only)
+- Type-safe IPC channels for LLM operations
+- Extensive model configuration and client adapters
+
+**File Management:**
+
+- Supports `.athignore` and `.gitignore` patterns
+- Chokidar file watchers for real-time updates
+- Path normalization via `PathUtils.ts`
+- Agent task creation in `.ath_materials` directory
+
+**CLI/Terminal Support:**
+
+- Integrated terminal via `node-pty` and `xterm.js`
+- Multi-session support with persistent terminals
+- Platform-specific shell detection (PowerShell on Windows, zsh/bash on Unix)
+- Managed by `ShellService.ts` and `cliStore.ts`
+
+**Additional Features:**
+
+- **Tooltips**: Contextual help throughout the UI via hover tooltips
+- **Drag and Drop**: File paths can be dragged from explorer to task/context areas
+- **Context Suggestions**: Automatic context suggestions based on task content
+- **Preset Tasks**: Pre-defined task templates loaded from `task_*.xml` files
+- **Token Budgeting**: Intelligent file inclusion based on token limits
+- **Smart Preview**: Configurable preview of file contents in prompts
+- **Documentation Format**: Multiple format options for file inclusion
+- **Ignore Rules**: Advanced pattern matching with `.athignore` and `.gitignore`
+- **Project Settings**: Stored in `.ath_materials/project_settings.json`
+
+## Testing Considerations
+
+**Mocking Strategy:**
+
+- Electron modules mocked via `tests/__mocks__/electron.ts`
+- File system operations mocked for isolation
+- Tests co-located with source files (e.g., `FileService.test.ts`)
+
+**Test Environment:**
+
+- Jest with Node.js environment for main process
+- ts-jest for TypeScript compilation
+- Tests cover both main and renderer processes
+
+## Development Guidelines
+
+**When adding file system features:**
+
+1. Add core functionality to `FileService.ts` or `PathUtils.ts`
+2. Create IPC handlers in `handlers/` directory
+3. Update `preload.ts` interface methods
+4. Update `src/types/global.d.ts` type definitions
+5. Implement UI-level operations in `fileSystemService.ts`
+
+**When adding new IPC handlers:**
+
+1. Create handler functions in appropriate file in `electron/handlers/`
+2. Export from `ipcHandlers.ts` for registration
+3. Add corresponding methods to `preload.ts`
+4. Update type definitions in `src/types/global.d.ts`
+
+**Important UI Patterns:**
+
+- **Left Panel**: File explorer with context menus and ignore functionality
+- **Right Panel**: Task tabs, file viewer, and Apply Changes panel
+- **Bottom Panel**: Log viewer with clickable entries for debugging
+- **Action Panel**: Controls for prompt generation, preset tasks, and settings toggles
+- **Task Templates**: XML-based templates in `resources/prompts/`
+- **Prompt Variants**: Context menu for switching between prompt modes (Query, Coder, Architect)
+
+**Security considerations:**
+
+- Never bypass IPC bridge for file operations
+- Validate all paths in main process handlers
+- Use secure API key storage for LLM integration
+
+**Code style:**
+
+- TypeScript 5+ with strict typing
+- Prettier for code formatting (ESLint config exists but is incompatible with ESLint 9+)
+- TailwindCSS 3 + Material-UI components
+- Conventional Commits for commit messages
+
+## Key Dependencies
+
+- **Electron 33+** - Desktop app framework
+- **React 19+** - UI framework
+- **TypeScript 5+** - Type safety
+- **Zustand** - State management
+- **Chokidar** - File watching
+- **ignore** - .gitignore/.athignore parsing
+- **js-tiktoken** - Token counting for prompts
+- **Jest + ts-jest** - Testing framework
+- **@anthropic-ai/sdk** - Anthropic Claude API integration
+- **openai** - OpenAI API integration
+- **@google/genai** - Google Gemini API integration
+- **node-pty** - Terminal emulation support
+- **xterm & xterm-addon-fit** - Terminal rendering in UI

From 86f46e79fbc4835ee3a29d56a09bbc6ba286ebea Mon Sep 17 00:00:00 2001
From: Luigi Acerbi <luigi.acerbi@gmail.com>
Date: Wed, 2 Jul 2025 14:52:27 +0200
Subject: [PATCH 13/13] chore: updated CHANGELOG.md

Signed-off-by: Luigi Acerbi <luigi.acerbi@gmail.com>
---
 CHANGELOG.md | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d787c21..78e01a0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,31 @@ and this project aims to adhere to [Semantic Versioning](https://semver.org/spec
 
 _(Future changes will go here)_
 
+### Added
+
+- A new `agent_task` command for advanced, agent-based workflows, including clickable log entries and dynamic prompt updates. ([a69b80c](https://github.com/lacerbi/athanor/commit/a69b80c), [94aa97f](https://github.com/lacerbi/athanor/commit/94aa97f), [67ba73e](https://github.com/lacerbi/athanor/commit/67ba73e))
+- Enhanced `CREATE` file operation to allow overwriting existing files with a clear user warning. ([4e2027a](https://github.com/lacerbi/athanor/commit/4e2027a))
+- Listeners for `Ctrl+C`/`Ctrl+V` to improve clipboard interaction. ([7743aa8](https://github.com/lacerbi/athanor/commit/7743aa8))
+
+### Changed
+
+- Updated the agentic architect prompt for better performance. ([4e2027a](https://github.com/lacerbi/athanor/commit/4e2027a))
+
+### Fixed
+
+- Corrected paste behavior within the application. ([bfb3a3e](https://github.com/lacerbi/athanor/commit/bfb3a3e))
+- Added `ELECTRON_USE_DESKTOP_GL` environment flag to mitigate potential rendering issues. ([87ba6e3](https://github.com/lacerbi/athanor/commit/87ba6e3))
+- Minor text clarifications in the Review panel for better usability. ([ef6d6d5](https://github.com/lacerbi/athanor/commit/ef6d6d5))
+
+### Documentation
+
+- Added `GEMINI.md` and updated `CLAUDE.md` to provide guidance for different AI models. ([b2f15cb](https://github.com/lacerbi/athanor/commit/b2f15cb), [fdc032d](https://github.com/lacerbi/athanor/commit/fdc032d))
+- Clarified that Prettier is used for code formatting. ([c02b34a](https://github.com/lacerbi/athanor/commit/c02b34a))
+
+### Tests
+
+- Fixed and updated unit tests to align with the new `agent_task` command. ([8050594](https://github.com/lacerbi/athanor/commit/8050594))
+
 ## [0.7.7] - 2025-07-01
 
 ### Added