diff --git a/docs/src/content/docs/integrations/ide-tool-integration.md b/docs/src/content/docs/integrations/ide-tool-integration.md
index bb7e0fe81..6c73ab091 100644
--- a/docs/src/content/docs/integrations/ide-tool-integration.md
+++ b/docs/src/content/docs/integrations/ide-tool-integration.md
@@ -57,7 +57,7 @@ For running agentic workflows locally, see the [Agent Workflows guide](../../gui
 
 APM works natively with VS Code's GitHub Copilot implementation.
 
-> **Auto-Detection**: VS Code integration is automatically enabled when a `.github/` folder exists in your project. If neither `.github/` nor `.claude/` exists, `apm install` skips folder integration (packages are still installed to `apm_modules/`). To force integration regardless of folder presence, pass an explicit target (e.g. `apm install --target copilot`) or set `target:` in `apm.yml` -- the target's root folder will be created automatically.
+> **Auto-Detection**: VS Code integration is automatically enabled when a `.github/` folder contains Copilot-specific markers (instructions, prompts, skills, agents, hooks, or chatmodes). A bare `.github/` with only CI workflows or CODEOWNERS will NOT trigger Copilot auto-detection. If no target folder is detected, `apm install` falls back to minimal mode (AGENTS.md only, no folder integration). To force integration regardless of folder presence, pass an explicit target (e.g. `apm install --target copilot`) or set `target:` in `apm.yml` -- the target's root folder will be created automatically.
 
 ### Native VS Code Primitives
 
diff --git a/docs/src/content/docs/introduction/how-it-works.md b/docs/src/content/docs/introduction/how-it-works.md
index bb511da98..b8f61d552 100644
--- a/docs/src/content/docs/introduction/how-it-works.md
+++ b/docs/src/content/docs/introduction/how-it-works.md
@@ -251,7 +251,7 @@ These tools support the full set of APM primitives. Running `apm install` deploy
 - **GitHub Copilot** (AGENTS.md + .github/) - instructions, prompts, chat modes, context, hooks, MCP
 - **Claude Code** (CLAUDE.md + .claude/) - commands, skills, MCP configuration
 
-APM auto-detects targets based on project structure -- deploying to every recognized directory (`.github/`, `.claude/`, `.cursor/`, `.opencode/`) that exists, falling back to `.github/` when none do. Set `target` in `apm.yml` to restrict to specific targets (single string or list).
+APM auto-detects targets based on project structure -- deploying to every recognized directory (`.github/`, `.claude/`, `.cursor/`, `.opencode/`) that exists, falling back to minimal (AGENTS.md only) when none do. For `.github/`, APM requires Copilot-specific markers (instructions, prompts, skills, agents, hooks, or chatmodes) to avoid false positives from repos that only use `.github/` for CI workflows. Set `target` in `apm.yml` to restrict to specific targets (single string or list).
 
 ### Compiled instructions
 
diff --git a/docs/src/content/docs/reference/cli-commands.md b/docs/src/content/docs/reference/cli-commands.md
index d9de84fff..49319017a 100644
--- a/docs/src/content/docs/reference/cli-commands.md
+++ b/docs/src/content/docs/reference/cli-commands.md
@@ -286,7 +286,7 @@ apm install --dry-run
 
 APM automatically detects which integrations to enable based on your project structure:
 
-- **VSCode integration**: Enabled when `.github/` directory exists
+- **VSCode integration**: Enabled when `.github/` contains Copilot-specific markers (instructions, prompts, skills, agents, hooks, or chatmodes)
 - **Claude integration**: Enabled when `.claude/` directory exists
 - **Cursor integration**: Enabled when `.cursor/` directory exists
 - **OpenCode integration**: Enabled when `.opencode/` directory exists
diff --git a/src/apm_cli/core/target_detection.py b/src/apm_cli/core/target_detection.py
index 6f2c977d5..00fdac8fc 100644
--- a/src/apm_cli/core/target_detection.py
+++ b/src/apm_cli/core/target_detection.py
@@ -119,7 +119,18 @@ def detect_target(  # noqa: PLR0911
             return "all", "apm.yml target"
 
     # Priority 3: Auto-detect from existing folders
-    github_exists = (project_root / ".github").exists()
+    # For .github/, require Copilot-specific markers (not just CI workflows).
+    # A bare .github/ with only workflows/CODEOWNERS/etc. is NOT a Copilot signal.
+    github_copilot_markers = [
+        ".github/copilot-instructions.md",
+        ".github/skills",
+        ".github/agents",
+        ".github/prompts",
+        ".github/instructions",
+        ".github/hooks",
+        ".github/chatmodes",
+    ]
+    github_exists = any((project_root / marker).exists() for marker in github_copilot_markers)
     claude_exists = (project_root / ".claude").exists()
     cursor_exists = (project_root / ".cursor").is_dir()
     opencode_exists = (project_root / ".opencode").is_dir()
diff --git a/tests/unit/core/test_target_detection.py b/tests/unit/core/test_target_detection.py
index c766274e0..22bc73770 100644
--- a/tests/unit/core/test_target_detection.py
+++ b/tests/unit/core/test_target_detection.py
@@ -6,6 +6,7 @@
 from apm_cli.core.target_detection import (
     ALL_CANONICAL_TARGETS,
     EXPERIMENTAL_TARGETS,
+    REASON_NO_TARGET_FOLDER,
     VALID_TARGET_VALUES,
     TargetParamType,
     detect_target,
@@ -123,8 +124,47 @@ def test_config_target_all(self, tmp_path):
         assert reason == "apm.yml target"
 
     def test_auto_detect_github_only(self, tmp_path):
-        """Auto-detect vscode when only .github/ exists."""
-        (tmp_path / ".github").mkdir()
+        """Auto-detect vscode when only .github/ with Copilot markers exists."""
+        (tmp_path / ".github" / "prompts").mkdir(parents=True)
+
+        target, reason = detect_target(
+            project_root=tmp_path,
+            explicit_target=None,
+            config_target=None,
+        )
+
+        assert target == "vscode"
+        assert "detected .github/ folder" in reason
+
+    def test_auto_detect_github_instructions_marker(self, tmp_path):
+        """Auto-detect vscode when .github/instructions/ exists."""
+        (tmp_path / ".github" / "instructions").mkdir(parents=True)
+
+        target, reason = detect_target(
+            project_root=tmp_path,
+            explicit_target=None,
+            config_target=None,
+        )
+
+        assert target == "vscode"
+        assert "detected .github/ folder" in reason
+
+    def test_auto_detect_github_hooks_marker(self, tmp_path):
+        """Auto-detect vscode when .github/hooks/ exists."""
+        (tmp_path / ".github" / "hooks").mkdir(parents=True)
+
+        target, reason = detect_target(
+            project_root=tmp_path,
+            explicit_target=None,
+            config_target=None,
+        )
+
+        assert target == "vscode"
+        assert "detected .github/ folder" in reason
+
+    def test_auto_detect_github_chatmodes_marker(self, tmp_path):
+        """Auto-detect vscode when .github/chatmodes/ exists."""
+        (tmp_path / ".github" / "chatmodes").mkdir(parents=True)
 
         target, reason = detect_target(
             project_root=tmp_path,
@@ -150,7 +190,7 @@ def test_auto_detect_claude_only(self, tmp_path):
 
     def test_auto_detect_both_folders(self, tmp_path):
         """Auto-detect all when both folders exist."""
-        (tmp_path / ".github").mkdir()
+        (tmp_path / ".github" / "prompts").mkdir(parents=True)
         (tmp_path / ".claude").mkdir()
 
         target, reason = detect_target(
@@ -164,6 +204,21 @@ def test_auto_detect_both_folders(self, tmp_path):
 
     def test_auto_detect_neither_folder(self, tmp_path):
         """Auto-detect minimal when neither folder exists."""
+        target, _reason = detect_target(
+            project_root=tmp_path,
+            explicit_target=None,
+            config_target=None,
+        )
+
+        assert target == "minimal"
+
+    def test_auto_detect_bare_github_no_copilot_markers(self, tmp_path):
+        """Auto-detect minimal when .github/ exists but has no Copilot markers.
+
+        A bare .github/ with only workflows/CODEOWNERS is NOT a Copilot signal.
+        """
+        (tmp_path / ".github" / "workflows").mkdir(parents=True)
+
         target, reason = detect_target(
             project_root=tmp_path,
             explicit_target=None,
@@ -171,7 +226,7 @@ def test_auto_detect_neither_folder(self, tmp_path):
         )
 
         assert target == "minimal"
-        assert "no target folder found" in reason
+        assert reason == REASON_NO_TARGET_FOLDER
 
 
 class TestShouldCompileAgentsMd:
@@ -360,8 +415,8 @@ def test_auto_detect_cursor_only(self, tmp_path):
         assert ".cursor/" in reason
 
     def test_auto_detect_cursor_plus_github(self, tmp_path):
-        """Auto-detect all when .cursor/ and .github/ exist."""
-        (tmp_path / ".github").mkdir()
+        """Auto-detect all when .cursor/ and .github/ with Copilot markers exist."""
+        (tmp_path / ".github" / "prompts").mkdir(parents=True)
         (tmp_path / ".cursor").mkdir()
         target, _ = detect_target(
             project_root=tmp_path,
@@ -399,8 +454,8 @@ def test_auto_detect_opencode_only(self, tmp_path):
         assert ".opencode/" in reason
 
     def test_auto_detect_opencode_plus_github(self, tmp_path):
-        """Auto-detect all when .opencode/ and .github/ exist."""
-        (tmp_path / ".github").mkdir()
+        """Auto-detect all when .opencode/ and .github/ with Copilot markers exist."""
+        (tmp_path / ".github" / "prompts").mkdir(parents=True)
         (tmp_path / ".opencode").mkdir()
         target, _ = detect_target(
             project_root=tmp_path,