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

main.js

@@ -8158,7 +8158,9 @@ var SemanticCacheService = class _SemanticCacheService {
         where: { source: "ollama" }
       });
       if (results.ids[0] && results.ids[0].length > 0) {
-        if (results.distances && results.distances[0] && results.distances[0][0] > this.config.similarityThreshold) {
+        const distance = results.distances?.[0]?.[0];
+        const similarity = typeof distance === "number" ? 1 - distance : 0;
+        if (similarity >= this.config.similarityThreshold) {
           return results.documents[0][0];
         }
       }
@@ -8940,14 +8942,12 @@ var ToolExecutor = class {
       return false;
     }
     const normalized = path.replace(/^(\.\/)+/, "");
-    if (normalized.split("/").includes("..")) {
+    const segments = normalized.split("/").filter((segment) => segment.length > 0);
+    if (segments.includes("..")) {
       return false;
     }
-    for (const dir of FORBIDDEN_DIRS) {
+    for (const segment of segments) {
-      if (normalized.startsWith(`${dir}/`) || normalized.startsWith(`${dir}\\`)) {
+      if (FORBIDDEN_DIRS.includes(segment)) {
-        return false;
-      }
-      if (normalized.includes(`/${dir}/`) || normalized.includes(`\\${dir}\\`)) {
         return false;
       }
     }
@@ -9930,6 +9930,7 @@ ${queryResult}`
 var VARIABLE_PATTERN = /\{\{([\w.]+)\}\}/g;
 var WorkflowEngine = class _WorkflowEngine {
   constructor(vault, app, ollamaUrl, model, options) {
+    this.availableTools = [];
     this.vaultIndexer = new VaultIndexer(vault);
     this.vaultIndexer.setApp(app);
     this.toolExecutor = new ToolExecutor(vault, app, void 0, this.vaultIndexer);
@@ -10041,6 +10042,7 @@ var WorkflowEngine = class _WorkflowEngine {
    */
   async executeWorkflowFromQuery(userQuery, availableTools) {
     Logger.info(`Generating workflow from query: ${userQuery}`, "workflow-engine");
+    this.availableTools = availableTools ?? [];
     const workflow = await this.generateWorkflowFromQuery(userQuery, availableTools);
     if (!workflow) {
       return {
@@ -10203,7 +10205,7 @@ Rules:
       role: "user",
       content: config.userPrompt
     });
-    const tools = config.includeToolCalls ? [] : [];
+    const tools = config.includeToolCalls ? this.availableTools : [];
     const response = await this.ollamaClient.chat(messages, tools);
     return response.content ?? "";
   }
@@ -10934,7 +10936,7 @@ var ErrorHandler = class {
 
 // src/chat-view.ts
 var ChatView = class extends import_obsidian5.ItemView {
-  constructor(leaf, settings, vectorStore, structuredMemoryManager, telemetryManager, chatHistoryManager, onModelChange) {
+  constructor(leaf, settings, vectorStore, structuredMemoryManager, telemetryManager, chatHistoryManager, onModelChange, onPersist) {
     super(leaf);
     // State
     this.messages = [];
@@ -11003,6 +11005,7 @@ var ChatView = class extends import_obsidian5.ItemView {
     this.telemetryManager = telemetryManager;
     this.chatHistoryManager = chatHistoryManager;
     this.onModelChange = onModelChange;
+    this.onPersist = onPersist;
     this.workflowEngine = new WorkflowEngine(
       this.app.vault,
       this.app,
@@ -11399,6 +11402,7 @@ var ChatView = class extends import_obsidian5.ItemView {
     const activeId = this.chatHistoryManager?.getActiveSessionId();
     if (activeId) {
       this.chatHistoryManager?.updateSession(activeId, { agentMode: mode });
+      this.onPersist?.();
     }
   }
   clearConversation() {
@@ -11446,6 +11450,7 @@ var ChatView = class extends import_obsidian5.ItemView {
       agentMode: this.currentAgentMode,
       title: this.deriveSessionTitle(nonStreamingMessages)
     });
+    this.onPersist?.();
   }
   syncMessagesToSession() {
     if (!this.chatHistoryManager) return;
@@ -11457,6 +11462,7 @@ var ChatView = class extends import_obsidian5.ItemView {
       agentMode: this.currentAgentMode,
       title: this.deriveSessionTitle(nonStreamingMessages)
     });
+    this.onPersist?.();
   }
   deriveSessionTitle(messages) {
     const firstUser = messages.find((m) => m.role === "user");
@@ -13359,6 +13365,9 @@ var AutoLinker = class {
   }
   updateConfig(config) {
     this.config = config;
+    if (typeof config.targetFolder === "string") {
+      this.targetFolder = config.targetFolder;
+    }
   }
   setTargetFolder(folder) {
     this.targetFolder = folder;
@@ -13902,7 +13911,8 @@ var OllamaPlugin = class extends import_obsidian7.Plugin {
           this.settings.model = model;
           void this.saveSettings();
           this.notifyChatViews();
-        }
+        },
+        () => this.scheduleSaveSettings()
       )
     );
     this.addRibbonIcon("bot", "Open Ollama Chat", async () => {
@@ -13958,7 +13968,7 @@ var OllamaPlugin = class extends import_obsidian7.Plugin {
         this.initializeAutoOrganizer();
         if (this.autoLinker) {
           new import_obsidian7.Notice("Auto-linking related notes...");
-          void this.autoLinker.run();
+          void this.autoLinker.run(this.settings.autoLinkConfig.dryRun);
         }
       }
     });
@@ -14007,9 +14017,11 @@ var OllamaPlugin = class extends import_obsidian7.Plugin {
   // eslint-disable-next-line @typescript-eslint/no-misused-promises
   onunload() {
     this.cancelBackgroundIndexing();
-    if (this.semanticCache) {
+    if (this.saveSettingsTimer) {
-      void this.semanticCache.clearCache();
+      clearTimeout(this.saveSettingsTimer);
+      this.saveSettingsTimer = void 0;
     }
+    void this.saveSettings();
   }
   async loadSettings() {
     const data = await this.loadData() ?? {};
@@ -14037,6 +14049,17 @@ var OllamaPlugin = class extends import_obsidian7.Plugin {
       chatHistory: this.chatHistoryManager?.getData() ?? createDefaultChatHistoryData()
     });
   }
+  scheduleSaveSettings(delayMs = 500) {
+    if (this.saveSettingsTimer) {
+      clearTimeout(this.saveSettingsTimer);
+    }
+    this.saveSettingsTimer = setTimeout(() => {
+      this.saveSettingsTimer = void 0;
+      void this.saveSettings().catch((error) => {
+        Logger.warn(`Failed to persist plugin data: ${String(error)}`, "main");
+      });
+    }, delayMs);
+  }
   initializeAutoOrganizer() {
     this.autoTagger = new AutoTagger(
       this.app.vault,
@@ -14150,26 +14173,32 @@ var OllamaPlugin = class extends import_obsidian7.Plugin {
       await this.vaultVectorStore.clearIndex();
     }
   }
+  indexVaultFileWhenReady(file) {
+    void (async () => {
+      await this.awaitBackgroundIndexing();
+      if (!this.vaultVectorStore) return;
+      const currentFile = this.app.vault.getAbstractFileByPath(file.path);
+      if (!(currentFile instanceof import_obsidian7.TFile) || currentFile.extension !== "md") return;
+      const content = await this.app.vault.read(currentFile);
+      const cache = this.app.metadataCache.getFileCache(currentFile);
+      await this.vaultVectorStore.indexFile(currentFile, content, cache ?? void 0);
+    })().catch((error) => {
+      const errorMessage = error instanceof Error ? error.message : String(error);
+      Logger.warn(`Failed to update vault index for ${file.path}: ${errorMessage}`, "main");
+    });
+  }
   registerVaultEventListeners() {
     this.registerEvent(
       this.app.vault.on("create", (file) => {
         if (file instanceof import_obsidian7.TFile && file.extension === "md" && this.vaultVectorStore) {
-          void this.app.vault.read(file).then((content) => {
+          this.indexVaultFileWhenReady(file);
-            if (!this.currentIndexingPromise) {
-              void this.vaultVectorStore?.indexFile(file, content);
-            }
-          });
         }
       })
     );
     this.registerEvent(
       this.app.vault.on("modify", (file) => {
         if (file instanceof import_obsidian7.TFile && file.extension === "md" && this.vaultVectorStore) {
-          void this.app.vault.read(file).then((content) => {
+          this.indexVaultFileWhenReady(file);
-            if (!this.currentIndexingPromise) {
-              void this.vaultVectorStore?.indexFile(file, content);
-            }
-          });
         }
       })
     );
@@ -14184,11 +14213,7 @@ var OllamaPlugin = class extends import_obsidian7.Plugin {
       this.app.vault.on("rename", (file, oldPath) => {
         if (file instanceof import_obsidian7.TFile && file.extension === "md" && this.vaultVectorStore) {
           void this.vaultVectorStore.deleteFile(oldPath);
-          void this.app.vault.read(file).then((content) => {
+          this.indexVaultFileWhenReady(file);
-            if (!this.currentIndexingPromise) {
-              void this.vaultVectorStore?.indexFile(file, content);
-            }
-          });
         }
       })
     );
@@ -14538,7 +14563,7 @@ var OllamaSettingTab = class extends import_obsidian7.PluginSettingTab {
         try {
           this.plugin.initializeAutoOrganizer();
           if (this.plugin.autoLinker) {
-            await this.plugin.autoLinker.run();
+            await this.plugin.autoLinker.run(this.plugin.settings.autoLinkConfig.dryRun);
           }
         } catch {
           new import_obsidian7.Notice("Auto-linking failed. Check console for details.");

src/auto-organizer.ts

@@ -362,8 +362,12 @@ export class AutoLinker {
     enabled: boolean;
     maxLinksPerNote: number;
     similarityThreshold: number;
+    targetFolder?: string;
   }): void {
     this.config = config;
+    if (typeof config.targetFolder === 'string') {
+      this.targetFolder = config.targetFolder;
+    }
   }
 
   setTargetFolder(folder: string): void {

src/chat-view.ts

@@ -58,7 +58,8 @@ export class ChatView extends ItemView {
     structuredMemoryManager?: StructuredMemoryManager,
     telemetryManager?: TelemetryManager,
     chatHistoryManager?: ChatHistoryManager,
-    onModelChange?: (model: string) => void
+    onModelChange?: (model: string) => void,
+    onPersist?: () => void
   ) {
     super(leaf);
     this.messages = [];
@@ -98,6 +99,7 @@ export class ChatView extends ItemView {
     this.telemetryManager = telemetryManager;
     this.chatHistoryManager = chatHistoryManager;
     this.onModelChange = onModelChange;
+    this.onPersist = onPersist;
     this.workflowEngine = new WorkflowEngine(
       this.app.vault,
       this.app,
@@ -565,6 +567,7 @@ export class ChatView extends ItemView {
     const activeId = this.chatHistoryManager?.getActiveSessionId();
     if (activeId) {
       this.chatHistoryManager?.updateSession(activeId, { agentMode: mode });
+      this.onPersist?.();
     }
   }
 
@@ -620,6 +623,7 @@ export class ChatView extends ItemView {
       agentMode: this.currentAgentMode,
       title: this.deriveSessionTitle(nonStreamingMessages),
     });
+    this.onPersist?.();
   }
 
   private syncMessagesToSession(): void {
@@ -632,6 +636,7 @@ export class ChatView extends ItemView {
       agentMode: this.currentAgentMode,
       title: this.deriveSessionTitle(nonStreamingMessages),
     });
+    this.onPersist?.();
   }
 
   private deriveSessionTitle(messages: ChatMessage[]): string {
@@ -1885,6 +1890,7 @@ export class ChatView extends ItemView {
   private chatHistoryManager?: ChatHistoryManager;
   private vectorStore?: VaultVectorStore;
   private onModelChange?: (model: string) => void;
+  private onPersist?: () => void;
 
   private modeSelectorEl: HTMLSelectElement | null = null;
   private modelSelectorEl: HTMLSelectElement | null = null;

src/main.ts

@@ -24,6 +24,7 @@ export default class OllamaPlugin extends Plugin {
   chatHistoryManager?: ChatHistoryManager;
   private indexingAbortController?: AbortController;
   private currentIndexingPromise?: Promise<void>;
+  private saveSettingsTimer?: ReturnType<typeof setTimeout>;
 
   async onload() {
     await this.loadSettings();
@@ -50,7 +51,8 @@ export default class OllamaPlugin extends Plugin {
             this.settings.model = model;
             void this.saveSettings();
             this.notifyChatViews();
-          }
+          },
+          () => this.scheduleSaveSettings()
         )
     );
 
@@ -120,7 +122,7 @@ export default class OllamaPlugin extends Plugin {
         this.initializeAutoOrganizer();
         if (this.autoLinker) {
           new Notice('Auto-linking related notes...');
-          void this.autoLinker.run();
+          void this.autoLinker.run(this.settings.autoLinkConfig.dryRun);
         }
       },
     });
@@ -182,11 +184,11 @@ export default class OllamaPlugin extends Plugin {
     // Cancel any ongoing indexing
     this.cancelBackgroundIndexing();
 
-    // Clean up any active semantic cache resources on plugin unload
+    if (this.saveSettingsTimer) {
-    // Using fire-and-forget pattern since onunload cannot be async per Obsidian API
+      clearTimeout(this.saveSettingsTimer);
-    if (this.semanticCache) {
+      this.saveSettingsTimer = undefined;
-      void this.semanticCache.clearCache();
     }
+    void this.saveSettings();
     // No explicit unregisterView needed; relying on Obsidian lifecycle management.
   }
 
@@ -227,6 +229,18 @@ export default class OllamaPlugin extends Plugin {
     });
   }
 
+  private scheduleSaveSettings(delayMs = 500): void {
+    if (this.saveSettingsTimer) {
+      clearTimeout(this.saveSettingsTimer);
+    }
+    this.saveSettingsTimer = setTimeout(() => {
+      this.saveSettingsTimer = undefined;
+      void this.saveSettings().catch((error) => {
+        Logger.warn(`Failed to persist plugin data: ${String(error)}`, 'main');
+      });
+    }, delayMs);
+  }
+
   initializeAutoOrganizer(): void {
     this.autoTagger = new AutoTagger(
       this.app.vault,
@@ -368,17 +382,30 @@ export default class OllamaPlugin extends Plugin {
     }
   }
 
+  private indexVaultFileWhenReady(file: TFile): void {
+    void (async () => {
+      await this.awaitBackgroundIndexing();
+
+      if (!this.vaultVectorStore) return;
+
+      const currentFile = this.app.vault.getAbstractFileByPath(file.path);
+      if (!(currentFile instanceof TFile) || currentFile.extension !== 'md') return;
+
+      const content = await this.app.vault.read(currentFile);
+      const cache = this.app.metadataCache.getFileCache(currentFile);
+      await this.vaultVectorStore.indexFile(currentFile, content, cache ?? undefined);
+    })().catch((error) => {
+      const errorMessage = error instanceof Error ? error.message : String(error);
+      Logger.warn(`Failed to update vault index for ${file.path}: ${errorMessage}`, 'main');
+    });
+  }
+
   registerVaultEventListeners(): void {
     // Listen for file creation
     this.registerEvent(
       this.app.vault.on('create', (file) => {
         if (file instanceof TFile && file.extension === 'md' && this.vaultVectorStore) {
-          void this.app.vault.read(file).then((content) => {
+          this.indexVaultFileWhenReady(file);
-            // Skip if a full rebuild is in progress to avoid race conditions
-            if (!this.currentIndexingPromise) {
-              void this.vaultVectorStore?.indexFile(file, content);
-            }
-          });
         }
       })
     );
@@ -387,11 +414,7 @@ export default class OllamaPlugin extends Plugin {
     this.registerEvent(
       this.app.vault.on('modify', (file) => {
         if (file instanceof TFile && file.extension === 'md' && this.vaultVectorStore) {
-          void this.app.vault.read(file).then((content) => {
+          this.indexVaultFileWhenReady(file);
-            if (!this.currentIndexingPromise) {
-              void this.vaultVectorStore?.indexFile(file, content);
-            }
-          });
         }
       })
     );
@@ -410,11 +433,7 @@ export default class OllamaPlugin extends Plugin {
       this.app.vault.on('rename', (file, oldPath) => {
         if (file instanceof TFile && file.extension === 'md' && this.vaultVectorStore) {
           void this.vaultVectorStore.deleteFile(oldPath);
-          void this.app.vault.read(file).then((content) => {
+          this.indexVaultFileWhenReady(file);
-            if (!this.currentIndexingPromise) {
-              void this.vaultVectorStore?.indexFile(file, content);
-            }
-          });
         }
       })
     );
@@ -938,7 +957,7 @@ class OllamaSettingTab extends PluginSettingTab {
           try {
             this.plugin.initializeAutoOrganizer();
             if (this.plugin.autoLinker) {
-              await this.plugin.autoLinker.run();
+              await this.plugin.autoLinker.run(this.plugin.settings.autoLinkConfig.dryRun);
             }
           } catch {
             new Notice('Auto-linking failed. Check console for details.');

src/semantic-cache.ts

@@ -47,11 +47,9 @@ export class SemanticCacheService {
       });
 
       if (results.ids[0] && results.ids[0].length > 0) {
-        if (
+        const distance = results.distances?.[0]?.[0];
-          results.distances &&
+        const similarity = typeof distance === 'number' ? 1 - distance : 0;
-          results.distances[0] &&
+        if (similarity >= this.config.similarityThreshold) {
-          results.distances[0][0] > this.config.similarityThreshold
-        ) {
           return results.documents[0][0];
         }
       }

src/tool-executor.ts

@@ -62,16 +62,14 @@ export class ToolExecutor {
 
     // Reject paths that traverse to parent directories
     const normalized = path.replace(/^(\.\/)+/, '');
-    if (normalized.split('/').includes('..')) {
+    const segments = normalized.split('/').filter((segment) => segment.length > 0);
+    if (segments.includes('..')) {
       return false;
     }
 
     // Reject forbidden directories
-    for (const dir of FORBIDDEN_DIRS) {
+    for (const segment of segments) {
-      if (normalized.startsWith(`${dir}/`) || normalized.startsWith(`${dir}\\`)) {
+      if (FORBIDDEN_DIRS.includes(segment)) {
-        return false;
-      }
-      if (normalized.includes(`/${dir}/`) || normalized.includes(`\\${dir}\\`)) {
         return false;
       }
     }

src/workflow-engine/workflow-engine.ts

@@ -45,6 +45,7 @@ export class WorkflowEngine {
   private conversationStateManager: ConversationStateManager;
   private maxSteps: number;
   private maxWorkflowDuration: number;
+  private availableTools: OllamaTool[] = [];
 
   constructor(
     vault: Vault,
@@ -200,6 +201,7 @@ export class WorkflowEngine {
     availableTools?: OllamaTool[]
   ): Promise<WorkflowExecutionResult> {
     Logger.info(`Generating workflow from query: ${userQuery}`, 'workflow-engine');
+    this.availableTools = availableTools ?? [];
 
     // First, ask the LLM to generate a workflow plan
     const workflow = await this.generateWorkflowFromQuery(userQuery, availableTools);
@@ -407,7 +409,7 @@ Rules:
     });
 
     // Determine if we should include tools
-    const tools = config.includeToolCalls ? [] : [];
+    const tools = config.includeToolCalls ? this.availableTools : [];
 
     const response = await this.ollamaClient.chat(messages, tools);
     return response.content ?? '';

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', () => {