diff --git a/src/core/available-tools.ts b/src/core/available-tools.ts
index 6b45b3ca6..f3dabe97d 100644
--- a/src/core/available-tools.ts
+++ b/src/core/available-tools.ts
@@ -13,12 +13,26 @@ import { AI_TOOLS, type AIToolOption } from './config.js';
  * Scans the project path for AI tool configuration directories and returns
  * the tools that are present.
  *
- * Checks for each tool's `skillsDir` (e.g., `.claude/`, `.cursor/`) at the
- * project root. Only tools with a `skillsDir` property are considered.
+ * For tools with `detectionPaths`, checks those specific paths (files or
+ * directories). Otherwise checks for the tool's `skillsDir` directory at
+ * the project root. Only tools with a `skillsDir` property are considered.
  */
 export function getAvailableTools(projectPath: string): AIToolOption[] {
   return AI_TOOLS.filter((tool) => {
     if (!tool.skillsDir) return false;
+
+    if (tool.detectionPaths && tool.detectionPaths.length > 0) {
+      // statSync without .isDirectory() — detection paths can be files or directories
+      return tool.detectionPaths.some((p) => {
+        try {
+          fs.statSync(path.join(projectPath, p));
+          return true;
+        } catch {
+          return false;
+        }
+      });
+    }
+
     const dirPath = path.join(projectPath, tool.skillsDir);
     try {
       return fs.statSync(dirPath).isDirectory();
diff --git a/src/core/config.ts b/src/core/config.ts
index f35f92861..bf852999e 100644
--- a/src/core/config.ts
+++ b/src/core/config.ts
@@ -15,6 +15,7 @@ export interface AIToolOption {
   available: boolean;
   successLabel?: string;
   skillsDir?: string; // e.g., '.claude' - /skills suffix per Agent Skills spec
+  detectionPaths?: string[]; // Override skillsDir for auto-detection; any path existing triggers detection
 }
 
 export const AI_TOOLS: AIToolOption[] = [
@@ -31,7 +32,7 @@ export const AI_TOOLS: AIToolOption[] = [
   { name: 'Cursor', value: 'cursor', available: true, successLabel: 'Cursor', skillsDir: '.cursor' },
   { name: 'Factory Droid', value: 'factory', available: true, successLabel: 'Factory Droid', skillsDir: '.factory' },
   { name: 'Gemini CLI', value: 'gemini', available: true, successLabel: 'Gemini CLI', skillsDir: '.gemini' },
-  { name: 'GitHub Copilot', value: 'github-copilot', available: true, successLabel: 'GitHub Copilot', skillsDir: '.github' },
+  { name: 'GitHub Copilot', value: 'github-copilot', available: true, successLabel: 'GitHub Copilot', skillsDir: '.github', detectionPaths: ['.github/copilot-instructions.md', '.github/instructions', '.github/workflows/copilot-setup-steps.yml', '.github/prompts', '.github/agents', '.github/skills', '.github/.mcp.json'] },
   { name: 'iFlow', value: 'iflow', available: true, successLabel: 'iFlow', skillsDir: '.iflow' },
   { name: 'Kilo Code', value: 'kilocode', available: true, successLabel: 'Kilo Code', skillsDir: '.kilocode' },
   { name: 'Kiro', value: 'kiro', available: true, successLabel: 'Kiro', skillsDir: '.kiro' },
diff --git a/test/core/available-tools.test.ts b/test/core/available-tools.test.ts
index fb2912eb5..83942dfb3 100644
--- a/test/core/available-tools.test.ts
+++ b/test/core/available-tools.test.ts
@@ -87,5 +87,66 @@ describe('available-tools', () => {
       expect(tools).toHaveLength(1);
       expect(tools[0].value).toBe('claude');
     });
+
+    it('should not detect GitHub Copilot from bare .github directory', async () => {
+      // .github/ exists in virtually every GitHub repo (for workflows, issue templates, etc.)
+      // A bare .github/ directory should NOT trigger Copilot detection
+      await fs.mkdir(path.join(testDir, '.github'), { recursive: true });
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).not.toContain('github-copilot');
+    });
+
+    it('should detect GitHub Copilot when copilot-instructions.md exists', async () => {
+      await fs.mkdir(path.join(testDir, '.github'), { recursive: true });
+      await fs.writeFile(path.join(testDir, '.github', 'copilot-instructions.md'), '');
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).toContain('github-copilot');
+    });
+
+    it('should detect GitHub Copilot when .github/prompts directory exists', async () => {
+      await fs.mkdir(path.join(testDir, '.github', 'prompts'), { recursive: true });
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).toContain('github-copilot');
+    });
+
+    it('should detect GitHub Copilot when .github/agents directory exists', async () => {
+      await fs.mkdir(path.join(testDir, '.github', 'agents'), { recursive: true });
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).toContain('github-copilot');
+    });
+
+    it('should detect GitHub Copilot when .github/skills directory exists', async () => {
+      await fs.mkdir(path.join(testDir, '.github', 'skills'), { recursive: true });
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).toContain('github-copilot');
+    });
+
+    it('should detect GitHub Copilot when copilot-setup-steps.yml exists', async () => {
+      await fs.mkdir(path.join(testDir, '.github', 'workflows'), { recursive: true });
+      await fs.writeFile(path.join(testDir, '.github', 'workflows', 'copilot-setup-steps.yml'), '');
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).toContain('github-copilot');
+    });
+
+    it('should still use skillsDir detection for tools without detectionPaths', async () => {
+      // Claude Code has no detectionPaths, so .claude/ directory should still work
+      await fs.mkdir(path.join(testDir, '.claude'), { recursive: true });
+
+      const tools = getAvailableTools(testDir);
+      const toolValues = tools.map((t) => t.value);
+      expect(toolValues).toContain('claude');
+    });
   });
 });
diff --git a/test/core/init.test.ts b/test/core/init.test.ts
index 6af92aed2..c2499e4d6 100644
--- a/test/core/init.test.ts
+++ b/test/core/init.test.ts
@@ -565,6 +565,7 @@ describe('InitCommand - profile and detection features', () => {
 
     // Directory detected only (not configured with OpenSpec)
     await fs.mkdir(path.join(testDir, '.github'), { recursive: true });
+    await fs.writeFile(path.join(testDir, '.github', 'copilot-instructions.md'), '');
 
     searchableMultiSelectMock.mockResolvedValue(['claude']);
 
@@ -587,6 +588,7 @@ describe('InitCommand - profile and detection features', () => {
   it('should preselect detected tools for first-time interactive setup', async () => {
     // First-time init: no openspec/ directory and no configured OpenSpec skills.
     await fs.mkdir(path.join(testDir, '.github'), { recursive: true });
+    await fs.writeFile(path.join(testDir, '.github', 'copilot-instructions.md'), '');
 
     searchableMultiSelectMock.mockResolvedValue(['github-copilot']);
 
diff --git a/test/core/update.test.ts b/test/core/update.test.ts
index c36ac3da8..f3d393d93 100644
--- a/test/core/update.test.ts
+++ b/test/core/update.test.ts
@@ -1644,6 +1644,7 @@ content
 
       // Create two unconfigured tool directories
       await fs.mkdir(path.join(testDir, '.github'), { recursive: true });
+      await fs.writeFile(path.join(testDir, '.github', 'copilot-instructions.md'), '');
       await fs.mkdir(path.join(testDir, '.windsurf'), { recursive: true });
 
       const consoleSpy = vi.spyOn(console, 'log');