Fix semantic cache distance calculation, tool path validation, and add deferred settings persistence

- Convert Chroma cosine distance to similarity (1 - distance) for correct threshold comparison
- Simplify forbidden directory check to match path segments instead of string prefixes
- Add debounced settings save via onPersist callback in ChatView to prevent data loss
- Fix workflow engine to pass availableTools to LLM when includeToolCalls is enabled
- Add targetFolder support to AutoLinker config and update tests
- Harden vault file indexing to await background indexing before processing create/modify/rename events

tests/auto-organizer.test.ts

@@ -366,6 +366,25 @@ describe('AutoLinker', () => {
       expect(mockVault.read).toHaveBeenCalledWith(files[0]);
     });
 
+    it('should update targetFolder through updateConfig', async () => {
+      linker.setTargetFolder('Projects');
+      linker.updateConfig({
+        enabled: true,
+        maxLinksPerNote: 3,
+        similarityThreshold: 0.5,
+        targetFolder: 'Archive',
+      });
+      const files = [{ path: 'Projects/note1.md' }, { path: 'Archive/note2.md' }] as any[];
+      mockVault.getMarkdownFiles.mockReturnValue(files);
+      mockVault.read.mockResolvedValue('Content');
+      mockIndexer.searchVault!.mockResolvedValue([]);
+
+      await linker.run();
+
+      expect(mockVault.read).toHaveBeenCalledTimes(1);
+      expect(mockVault.read).toHaveBeenCalledWith(files[1]);
+    });
+
     it('should return dry-run proposals when dryRun is true', async () => {
       const files = [{ path: 'note.md' }] as any[];
       mockVault.getMarkdownFiles.mockReturnValue(files);

tests/semantic-cache.test.ts

@@ -119,7 +119,7 @@ describe('SemanticCacheService', () => {
       mockCollection.query.mockResolvedValue({
         ids: [['test-id']],
         documents: [[cachedContent]],
-        distances: [[0.9]], // Above threshold
+        distances: [[0.1]], // Similarity 0.9, above threshold
       });
 
       const result = await cacheService.getCache('test query');
@@ -127,6 +127,18 @@ describe('SemanticCacheService', () => {
       expect(result).toBe(cachedContent);
       expect(mockCollection.query).toHaveBeenCalled();
     });
+
+    it('should return null when cosine distance is too high', async () => {
+      mockCollection.query.mockResolvedValue({
+        ids: [['test-id']],
+        documents: [['unrelated cached response']],
+        distances: [[0.9]], // Similarity 0.1, below threshold
+      });
+
+      const result = await cacheService.getCache('test query');
+
+      expect(result).toBeNull();
+    });
   });
 
   describe('setCache', () => {

tests/tool-executor.test.ts

@@ -213,6 +213,38 @@ describe('ToolExecutor', () => {
         expect(mockVault.create).not.toHaveBeenCalled();
       });
 
+      it('should reject exact forbidden directory paths', async () => {
+        const call: ToolCall = {
+          id: 'call_forbidden_exact',
+          type: 'function',
+          function: {
+            name: 'create_file',
+            arguments: JSON.stringify({
+              path: '.obsidian',
+              content: 'Test content',
+            }),
+          },
+        };
+        await expect(executor.handleToolCall(call)).rejects.toThrow();
+        expect(mockVault.create).not.toHaveBeenCalled();
+      });
+
+      it('should reject nested forbidden directory paths', async () => {
+        const call: ToolCall = {
+          id: 'call_forbidden_nested',
+          type: 'function',
+          function: {
+            name: 'create_file',
+            arguments: JSON.stringify({
+              path: 'Notes/.git',
+              content: 'Test content',
+            }),
+          },
+        };
+        await expect(executor.handleToolCall(call)).rejects.toThrow();
+        expect(mockVault.create).not.toHaveBeenCalled();
+      });
+
       it('should reject path traversal attempts with .\\', async () => {
         const call: ToolCall = {
           id: 'call_8',
@@ -1214,6 +1246,22 @@ describe('ToolExecutor', () => {
         expect(mockVault.createFolder).toHaveBeenCalledWith('Archive');
         expect(mockVault.rename).toHaveBeenCalledWith(file, 'Archive/old.md');
       });
+
+      it('should reject moving a note into a forbidden folder', async () => {
+        const call: ToolCall = {
+          id: 'call_mn_forbidden',
+          type: 'function',
+          function: {
+            name: 'move_note',
+            arguments: JSON.stringify({
+              path: 'Projects/old.md',
+              folder: '.obsidian',
+            }),
+          },
+        };
+        await expect(executor.handleToolCall(call)).rejects.toThrow('Invalid folder path detected');
+        expect(mockVault.rename).not.toHaveBeenCalled();
+      });
     });
 
     describe('delete_note tool', () => {