fix: treat .github/-only auto-detection as ambiguous

.codex/config.toml

@@ -0,0 +1,25 @@
+[mcp_servers.github-mcp-server]
+command = "docker"
+args = [ "run", "-i", "--rm", "-e", "GITHUB_DYNAMIC_TOOLSETS", "-e", "GITHUB_PERSONAL_ACCESS_TOKEN", "-e", "GITHUB_TOOLSETS", "ghcr.io/github/github-mcp-server",]
+id = "ab12cd34-5678-90ef-1234-567890abcdef"
+
+[mcp_servers.notion-mcp-server]
+command = "npx"
+args = [ "-y", "@notionhq/notion-mcp-server@1.8.1", "--transport", "stdio", "--port", "3000", "secret_notion_token_67890",]
+id = "8b9c1d20-2345-6789-abcd-ef0123456789"
+
+[mcp_servers.test-docker-server]
+command = "docker"
+args = [ "run", "-i", "--rm", "example/test-server", "--verbose", "--config", "-e", "TEST_TOKEN", "/app/config.json",]
+id = "test-docker-with-pkg-args"
+
+[mcp_servers.github-mcp-server.env]
+GITHUB_PERSONAL_ACCESS_TOKEN = "ghp_token_123"
+GITHUB_TOOLSETS = "context"
+GITHUB_DYNAMIC_TOOLSETS = "1"
+
+[mcp_servers.notion-mcp-server.env]
+NOTION_TOKEN = "secret_notion_token_67890"
+
+[mcp_servers.test-docker-server.env]
+TEST_TOKEN = "test_token_value"

src/apm_cli/core/target_detection.py

@@ -8,7 +8,8 @@
 1. Explicit --target flag (always wins)
 2. apm.yml target setting (top-level field)
 3. Auto-detect from existing folders:
-   - .github/ only -> copilot (internal: "vscode")
+   - .github/ only -> minimal (ambiguous; .github/ is too common for CI
+     to reliably infer Copilot — user should set target explicitly)
    - .claude/ only -> claude
    - .cursor/ only -> cursor
    - .opencode/ only -> opencode
@@ -86,6 +87,12 @@ def agents_alias_was_detected() -> bool:
 # instead of substring matching.
 REASON_NO_TARGET_FOLDER = "no target folder found"
 
+# Detection reason returned by detect_target() when only .github/ exists but
+# no explicit or config target is set.  .github/ is too common (CI workflows,
+# issue templates, CODEOWNERS) to reliably infer Copilot usage — treat it as
+# ambiguous and ask the user to declare their target explicitly.
+REASON_AMBIGUOUS_GITHUB = "ambiguous .github/ — set target in apm.yml or use --target"
+
 # User-facing target values (includes aliases accepted by CLI)
 UserTargetType = Literal[
     "copilot",
@@ -189,7 +196,10 @@ def detect_target(  # noqa: PLR0911
     if len(detected) >= 2:
         return "all", f"detected {' and '.join(detected)} folders"
     elif github_exists:
-        return "vscode", "detected .github/ folder"
+        # .github/ alone is too ambiguous to infer Copilot — most repos have
+        # it for CI workflows, issue templates, CODEOWNERS, etc.  Return
+        # minimal so the user is prompted to set target explicitly.
+        return "minimal", REASON_AMBIGUOUS_GITHUB
     elif claude_exists:
         return "claude", "detected .claude/ folder"
     elif cursor_exists:

tests/unit/core/test_target_detection.py

@@ -124,8 +124,8 @@ def test_config_target_all(self, tmp_path):
         assert target == "all"
         assert reason == "apm.yml target"
 
-    def test_auto_detect_github_only(self, tmp_path):
-        """Auto-detect vscode when only .github/ exists."""
+    def test_auto_detect_github_only_returns_minimal(self, tmp_path):
+        """Auto-detect minimal when only .github/ exists (ambiguous)."""
         (tmp_path / ".github").mkdir()
 
         target, reason = detect_target(
@@ -134,8 +134,8 @@ def test_auto_detect_github_only(self, tmp_path):
             config_target=None,
         )
 
-        assert target == "vscode"
-        assert "detected .github/ folder" in reason
+        assert target == "minimal"
+        assert "ambiguous" in reason
 
     def test_auto_detect_claude_only(self, tmp_path):
         """Auto-detect claude when only .claude/ exists."""
@@ -176,6 +176,63 @@ def test_auto_detect_neither_folder(self, tmp_path):
         assert "no target folder found" in reason
 
 
+class TestDetectTargetAmbiguousGithub:
+    """Tests for .github/-only auto-detection returning minimal (ambiguous)."""
+
+    def test_github_only_returns_minimal(self, tmp_path):
+        """Only .github/ present — too ambiguous to assume Copilot."""
+        (tmp_path / ".github").mkdir()
+        target, reason = detect_target(project_root=tmp_path)
+        assert target == "minimal"
+        assert "ambiguous" in reason
+
+    def test_github_only_reason_mentions_set_target(self, tmp_path):
+        """Reason message should guide user to set target explicitly."""
+        (tmp_path / ".github").mkdir()
+        _, reason = detect_target(project_root=tmp_path)
+        assert "apm.yml" in reason or "--target" in reason
+
+    def test_github_only_explicit_copilot_wins(self, tmp_path):
+        """Explicit --target copilot overrides ambiguous .github/ detection."""
+        (tmp_path / ".github").mkdir()
+        target, reason = detect_target(
+            project_root=tmp_path, explicit_target="copilot"
+        )
+        assert target == "vscode"
+        assert "explicit" in reason
+
+    def test_github_only_config_copilot_wins(self, tmp_path):
+        """Config target: copilot overrides ambiguous .github/ detection."""
+        (tmp_path / ".github").mkdir()
+        target, reason = detect_target(
+            project_root=tmp_path, config_target="copilot"
+        )
+        assert target == "vscode"
+        assert "apm.yml" in reason
+
+    def test_github_plus_claude_returns_all(self, tmp_path):
+        """Multiple folders (.github/ + .claude/) still returns all."""
+        (tmp_path / ".github").mkdir()
+        (tmp_path / ".claude").mkdir()
+        target, reason = detect_target(project_root=tmp_path)
+        assert target == "all"
+        assert ".github/" in reason and ".claude/" in reason
+
+    def test_github_plus_cursor_returns_all(self, tmp_path):
+        """Multiple folders (.github/ + .cursor/) still returns all."""
+        (tmp_path / ".github").mkdir()
+        (tmp_path / ".cursor").mkdir()
+        target, _ = detect_target(project_root=tmp_path)
+        assert target == "all"
+
+    def test_reason_ambiguous_constant_defined(self):
+        """REASON_AMBIGUOUS_GITHUB is importable and non-empty."""
+        from apm_cli.core.target_detection import REASON_AMBIGUOUS_GITHUB
+
+        assert REASON_AMBIGUOUS_GITHUB
+        assert "ambiguous" in REASON_AMBIGUOUS_GITHUB
+
+
 class TestShouldCompileAgentsMd:
     """Tests for should_compile_agents_md function."""