Merge pull request #222 from fa1k3/fix/graph-ignore-exclusion

fix(graph): honor MCP ignore exclusions in graph traversal

src/tools/graph-search.ts

@@ -95,7 +95,15 @@ export class GraphSearchTool {
   private graphTraversal: GraphTraversal;
   
   constructor(private api: ObsidianAPI, private app: App) {
-    this.graphTraversal = new GraphTraversal(app);
+    this.graphTraversal = new GraphTraversal(app, api.getIgnoreManager());
+  }
+
+  /** Throw "File not found" for an ignored query root ('/' and '' are the virtual root). */
+  private assertNotExcluded(path?: string): void {
+    if (!path || path === '/') return;
+    if (this.graphTraversal.isExcluded(path)) {
+      throw new Error(`File not found: ${path}`);
+    }
   }
 
   /**
@@ -103,7 +111,14 @@ export class GraphSearchTool {
    */
   search(params: GraphSearchParams): GraphSearchResult {
     const { operation } = params;
-    
+
+    // Reject excluded query roots so directly targeting an ignored note does
+    // not disclose its relationships. Excluded paths are treated as not found,
+    // matching ObsidianAPI's read-path behavior. The '/' and '' sentinels are
+    // the virtual vault root, not real paths.
+    this.assertNotExcluded(params.sourcePath);
+    this.assertNotExcluded(params.targetPath);
+
     switch (operation) {
       case 'traverse':
         return this.performTraversal(params);
@@ -174,7 +189,7 @@ export class GraphSearchTool {
       edges: result.edges,
       graphStats: result.stats,
       message: params.sourcePath === '/' || params.sourcePath === ''
-        ? `Traversed from ${Math.min(10, this.app.vault.getFiles().length)} most recent files: Found ${result.stats.totalNodes} connected nodes within ${params.maxDepth} degrees`
+        ? `Traversed from ${Math.min(10, this.app.vault.getFiles().filter(f => !this.graphTraversal.isExcluded(f.path)).length)} most recent files: Found ${result.stats.totalNodes} connected nodes within ${params.maxDepth} degrees`
         : `Found ${result.stats.totalNodes} connected nodes within ${params.maxDepth} degrees of separation`,
       workflow: {
         message: 'Graph traversal complete. You can explore individual nodes or find paths between them.',

src/utils/graph-traversal.ts

@@ -1,4 +1,5 @@
 import { App, TFile, CachedMetadata, getAllTags } from 'obsidian';
+import { MCPIgnoreManager } from '../security/mcp-ignore-manager';
 
 /**
  * Represents a node in the Obsidian vault graph
@@ -53,7 +54,23 @@ export interface GraphTraversalResult {
  * Utility class for traversing the Obsidian vault graph
  */
 export class GraphTraversal {
-  constructor(private app: App) {}
+  constructor(private app: App, private ignoreManager?: MCPIgnoreManager) {}
+
+  /**
+   * Whether a path is excluded by the MCP ignore configuration.
+   *
+   * Graph traversal reads directly from metadataCache.resolvedLinks and
+   * vault.getFiles(), both unaware of .mcpignore. Excluded paths must be kept
+   * out of results on two fronts: the link primitives filter the far endpoint
+   * (so an ignored note never appears as a neighbor/edge of a visible query),
+   * and the file enumerations (getAllNodes, tag connections, root traversal,
+   * vault statistics) skip ignored files. The query root itself is rejected at
+   * the GraphSearchTool boundary, so directly querying an ignored note does not
+   * disclose its relationships. Public so that boundary can reuse this check.
+   */
+  isExcluded(path: string): boolean {
+    return !!this.ignoreManager && this.ignoreManager.isExcluded(path);
+  }
 
   /**
    * Get a human-friendly graph node title for a file.
@@ -84,7 +101,7 @@ export class GraphTraversal {
    * Get all nodes (files) in the vault
    */
   getAllNodes(): GraphNode[] {
-    const files = this.app.vault.getFiles();
+    const files = this.app.vault.getFiles().filter(f => !this.isExcluded(f.path));
     return files.map(file => ({
       file,
       path: file.path,
@@ -102,6 +119,7 @@ export class GraphTraversal {
 
     // Search through all files for links to this file
     for (const sourcePath in resolvedLinks) {
+      if (this.isExcluded(sourcePath)) continue;
       const links = resolvedLinks[sourcePath];
       if (links[filePath]) {
         edges.push({
@@ -125,6 +143,7 @@ export class GraphTraversal {
 
     if (links) {
       for (const targetPath in links) {
+        if (this.isExcluded(targetPath)) continue;
         edges.push({
           source: filePath,
           target: targetPath,
@@ -167,7 +186,7 @@ export class GraphTraversal {
     const edges: GraphEdge[] = [];
     const file = this.app.vault.getAbstractFileByPath(filePath);
 
-    if (!(file instanceof TFile)) return edges;
+    if (!(file instanceof TFile) || this.isExcluded(filePath)) return edges;
 
     const cache = this.app.metadataCache.getFileCache(file);
     const fileTags = new Set(cache ? getAllTags(cache) || [] : []);
@@ -177,6 +196,7 @@ export class GraphTraversal {
     const files = this.app.vault.getFiles();
     for (const otherFile of files) {
       if (otherFile.path === filePath) continue;
+      if (this.isExcluded(otherFile.path)) continue;
 
       const otherCache = this.app.metadataCache.getFileCache(otherFile);
       const otherTags = otherCache ? getAllTags(otherCache) || [] : [];
@@ -224,7 +244,9 @@ export class GraphTraversal {
       const allFiles = this.app.vault.getFiles();
 
       // Sort by modification time to get most relevant files first
-      const sortedFiles = allFiles.sort((a, b) => b.stat.mtime - a.stat.mtime);
+      const sortedFiles = allFiles
+        .filter(file => !this.isExcluded(file.path))
+        .sort((a, b) => b.stat.mtime - a.stat.mtime);
 
       // Take up to 10 most recently modified files as starting points
       const startingFiles = sortedFiles.slice(0, Math.min(10, sortedFiles.length));
@@ -256,7 +278,8 @@ export class GraphTraversal {
       const { path, depth } = queue.shift()!;
       
       if (visited.has(path) || depth > maxDepth) continue;
-      
+      if (this.isExcluded(path)) continue;
+
       const file = this.app.vault.getAbstractFileByPath(path);
       if (!(file instanceof TFile)) continue;
 
@@ -411,7 +434,7 @@ export class GraphTraversal {
     // Handle root path "/" specially
     if (filePath === '/' || filePath === '') {
       // For root, return a virtual node representing the vault with recent files as neighbors
-      const allFiles = this.app.vault.getFiles();
+      const allFiles = this.app.vault.getFiles().filter(f => !this.isExcluded(f.path));
       const sortedFiles = allFiles.sort((a, b) => b.stat.mtime - a.stat.mtime);
       const recentFiles = sortedFiles.slice(0, Math.min(20, sortedFiles.length));
 
@@ -502,7 +525,7 @@ export class GraphTraversal {
     largestComponentSize: number;
     isolatedClusters: number;
   } {
-    const mdFiles = this.app.vault.getFiles().filter(f => f.extension === 'md');
+    const mdFiles = this.app.vault.getFiles().filter(f => f.extension === 'md' && !this.isExcluded(f.path));
     const totalNotes = mdFiles.length;
 
     const resolved = this.app.metadataCache.resolvedLinks ?? {};

src/utils/obsidian-api.ts

@@ -100,6 +100,11 @@ export class ObsidianAPI {
     return this.app;
   }
 
+  // Getter to access the ignore manager so graph traversal can honor exclusions
+  getIgnoreManager(): MCPIgnoreManager | undefined {
+    return this.ignoreManager;
+  }
+
   // Server info
   getServerInfo() {
     const baseInfo = {

tests/graph-ignore-exclusion.test.ts

@@ -0,0 +1,142 @@
+import { App, TFile } from 'obsidian';
+import { GraphTraversal } from '../src/utils/graph-traversal';
+import { GraphSearchTool } from '../src/tools/graph-search';
+import { ObsidianAPI } from '../src/utils/obsidian-api';
+import { MCPIgnoreManager } from '../src/security/mcp-ignore-manager';
+
+function makeFile(path: string): TFile {
+  const file = new TFile();
+  file.path = path;
+  file.name = path.split('/').pop() ?? path;
+  file.basename = file.name.replace(/\.md$/, '');
+  file.extension = 'md';
+  (file as any).stat = { mtime: 0, ctime: 0, size: 0 };
+  return file;
+}
+
+// Fake ignore manager that excludes anything under _build/backups/
+const ignoreManager = {
+  isExcluded: (path: string) => path.startsWith('_build/backups/')
+} as unknown as MCPIgnoreManager;
+
+const FILES: Record<string, TFile> = {
+  'stack/index.md': makeFile('stack/index.md'),
+  'real.md': makeFile('real.md'),
+  '_build/backups/snapshot.md': makeFile('_build/backups/snapshot.md'),
+  '_build/backups/old.md': makeFile('_build/backups/old.md')
+};
+
+// Per-path tag cache — all four notes share #archived
+const TAGS: Record<string, string> = {
+  'stack/index.md': '#archived',
+  'real.md': '#archived',
+  '_build/backups/snapshot.md': '#archived',
+  '_build/backups/old.md': '#archived'
+};
+
+function makeApp(): App {
+  const app = new App();
+  (app as any).metadataCache = {
+    resolvedLinks: {
+      // stack/index.md links out to a real note AND a backup note
+      'stack/index.md': { 'real.md': 1, '_build/backups/old.md': 1 },
+      // a backup snapshot links back into stack/index.md
+      '_build/backups/snapshot.md': { 'stack/index.md': 1 },
+      'real.md': { 'stack/index.md': 1 }
+    },
+    unresolvedLinks: {},
+    getFileCache: jest.fn((file: any) => ({
+      tags: TAGS[file?.path] ? [{ tag: TAGS[file.path] }] : []
+    }))
+  };
+  app.vault.getAbstractFileByPath = jest.fn((path: string) => FILES[path] ?? null);
+  app.vault.getFiles = jest.fn(() => Object.values(FILES));
+  return app;
+}
+
+/**
+ * Graph traversal reads metadataCache.resolvedLinks and vault.getFiles()
+ * directly, both unaware of .mcpignore. These tests pin that ignored paths are
+ * kept out of (a) the link primitives, (b) the file enumerations (root, tags,
+ * vault stats, all-nodes), and (c) are rejected as query roots at the
+ * GraphSearchTool boundary so a direct query can't disclose their relationships.
+ */
+describe('GraphTraversal — link primitives & enumerations honor exclusions', () => {
+  let app: App;
+  beforeEach(() => { app = makeApp(); });
+
+  it('filters excluded sources out of backlinks', () => {
+    const sources = new GraphTraversal(app, ignoreManager).getBacklinks('stack/index.md').map(e => e.source);
+    expect(sources).toContain('real.md');
+    expect(sources).not.toContain('_build/backups/snapshot.md');
+  });
+
+  it('filters excluded targets out of forward links', () => {
+    const targets = new GraphTraversal(app, ignoreManager).getForwardLinks('stack/index.md').map(e => e.target);
+    expect(targets).toContain('real.md');
+    expect(targets).not.toContain('_build/backups/old.md');
+  });
+
+  it('keeps excluded nodes out of the local neighborhood', () => {
+    const { neighbors, edges } = new GraphTraversal(app, ignoreManager).getLocalNeighborhood('stack/index.md');
+    const paths = neighbors.map(n => n.path);
+    expect(paths).toContain('real.md');
+    expect(paths).not.toContain('_build/backups/old.md');
+    expect(paths).not.toContain('_build/backups/snapshot.md');
+    expect(edges.every(e => !e.source.startsWith('_build/backups/') && !e.target.startsWith('_build/backups/'))).toBe(true);
+  });
+
+  it('excludes ignored files from the root neighborhood', () => {
+    const { neighbors } = new GraphTraversal(app, ignoreManager).getLocalNeighborhood('/');
+    expect(neighbors.map(n => n.path).some(p => p.startsWith('_build/backups/'))).toBe(false);
+  });
+
+  it('excludes ignored files from getAllNodes', () => {
+    const paths = new GraphTraversal(app, ignoreManager).getAllNodes().map(n => n.path);
+    expect(paths).toContain('stack/index.md');
+    expect(paths.some(p => p.startsWith('_build/backups/'))).toBe(false);
+  });
+
+  it('excludes ignored files from tag connections', () => {
+    const targets = new GraphTraversal(app, ignoreManager).getTagConnections('stack/index.md').map(e => e.target);
+    expect(targets).toContain('real.md');
+    expect(targets.some(p => p.startsWith('_build/backups/'))).toBe(false);
+  });
+
+  it('excludes ignored files from vault statistics totalNotes', () => {
+    // 4 files total, 2 under _build/backups/ → only 2 visible notes
+    expect(new GraphTraversal(app, ignoreManager).getVaultStatistics().totalNotes).toBe(2);
+  });
+
+  it('leaves everything unfiltered when no ignore manager is configured', () => {
+    const t = new GraphTraversal(app);
+    expect(t.getForwardLinks('stack/index.md').map(e => e.target)).toContain('_build/backups/old.md');
+    expect(t.getBacklinks('stack/index.md').map(e => e.source)).toContain('_build/backups/snapshot.md');
+    expect(t.getVaultStatistics().totalNotes).toBe(4);
+  });
+});
+
+describe('GraphSearchTool — rejects excluded query roots (no relationship disclosure)', () => {
+  let tool: GraphSearchTool;
+  beforeEach(() => {
+    const app = makeApp();
+    tool = new GraphSearchTool({ getIgnoreManager: () => ignoreManager } as unknown as ObsidianAPI, app);
+  });
+
+  for (const operation of ['backlinks', 'forwardlinks', 'neighbors', 'statistics'] as const) {
+    it(`throws "File not found" for ${operation} on an excluded sourcePath`, () => {
+      expect(() => tool.search({ operation, sourcePath: '_build/backups/snapshot.md' }))
+        .toThrow(/File not found/);
+    });
+  }
+
+  it('throws "File not found" for path when targetPath is excluded', () => {
+    expect(() => tool.search({ operation: 'path', sourcePath: 'real.md', targetPath: '_build/backups/old.md' }))
+      .toThrow(/File not found/);
+  });
+
+  it('does not reject the "/" vault root, and the root excludes ignored neighbors', () => {
+    const result = tool.search({ operation: 'neighbors', sourcePath: '/' });
+    expect((result.nodes ?? []).map(n => n.path).some(p => p.startsWith('_build/backups/'))).toBe(false);
+  });
+});

tests/graph-node-title.test.ts

@@ -47,7 +47,7 @@ describe('graph node titles', () => {
     app.vault.getAbstractFileByPath = jest.fn((path: string) => filesByPath.get(path) ?? null);
 
     traversal = new GraphTraversal(app);
-    search = new GraphSearchTool({} as ObsidianAPI, app);
+    search = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
   });
 
   it('uses the parent folder as the graph title for index files', () => {

tests/graph-search-traversal.test.ts

@@ -17,7 +17,7 @@ const mockApp = {
     }
 } as unknown as App;
 
-const mockAPI = {} as ObsidianAPI;
+const mockAPI = { getIgnoreManager: () => undefined } as unknown as ObsidianAPI;
 const mockSearchCore = new SearchCore(mockApp);
 
 describe('GraphSearchTraversal', () => {

tests/graph-search.test.ts

@@ -34,7 +34,7 @@ describe('GraphSearchTool', () => {
       path === 'resolved.md' ? resolvedTarget : null
     );
 
-    tool = new GraphSearchTool({} as ObsidianAPI, app);
+    tool = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
   });
 
   it('omits unresolved forward links by default', () => {

tests/graph-statistics-vault-wide.test.ts

@@ -58,7 +58,7 @@ describe('graph.statistics — vault-wide (#132)', () => {
         'd.md': { 'e.md': 1 },
       },
     });
-    tool = new GraphSearchTool({} as ObsidianAPI, app);
+    tool = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
   });
 
   it('returns vaultStatistics when sourcePath is omitted', () => {
@@ -95,7 +95,7 @@ describe('graph.statistics — vault-wide (#132)', () => {
       files: [A, B],
       resolvedLinks: { 'a.md': { 'b.md': 3 } },
     });
-    const t = new GraphSearchTool({} as ObsidianAPI, app);
+    const t = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
 
     const result = t.search({ operation: 'statistics' });
     expect(result.vaultStatistics).toMatchObject({
@@ -108,7 +108,7 @@ describe('graph.statistics — vault-wide (#132)', () => {
 
   it('handles an empty vault without dividing by zero', () => {
     const app = buildApp({ files: [], resolvedLinks: {} });
-    const t = new GraphSearchTool({} as ObsidianAPI, app);
+    const t = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
 
     const result = t.search({ operation: 'statistics' });
     expect(result.vaultStatistics).toEqual({
@@ -127,7 +127,7 @@ describe('graph.statistics — vault-wide (#132)', () => {
       files: [A, B, image],
       resolvedLinks: { 'a.md': { 'b.md': 1 } },
     });
-    const t = new GraphSearchTool({} as ObsidianAPI, app);
+    const t = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
 
     const result = t.search({ operation: 'statistics' });
     expect(result.vaultStatistics?.totalNotes).toBe(2);
@@ -142,7 +142,7 @@ describe('graph.statistics — vault-wide (#132)', () => {
         'b.md': { 'a.md': 1 },
       },
     });
-    const t = new GraphSearchTool({} as ObsidianAPI, app);
+    const t = new GraphSearchTool({ getIgnoreManager: () => undefined } as unknown as ObsidianAPI, app);
 
     const result = t.search({ operation: 'statistics' });
     expect(result.vaultStatistics).toMatchObject({