diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5c6f48c56..7693837b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- **`apm compile -t copilot` now emits `.github/copilot-instructions.md` with zero user configuration** -- APM's first Copilot-native compile target. Global instructions in `.apm/instructions/` are assembled into the file VS Code and GitHub Copilot read automatically; switching targets cleans it up. APM dogfoods this target. (#1048)
 - **`apm marketplace add` accepts full HTTPS URLs and nested HOST/group/sub/.../REPO shorthands.** You can now paste a repository URL straight from the browser (e.g., `apm marketplace add https://github.com/acme/plugin-marketplace`) and register marketplaces hosted under nested sub-paths on GitHub Enterprise (`ghes.corp.example.com/org/team/repo`). Path-traversal sequences in the parsed segments are rejected via `validate_path_segments`. Non-GitHub hosts (GitLab, Bitbucket, etc.) are explicitly rejected at registration time with an actionable error -- this avoids forwarding GitHub credentials to unintended hosts and the silent fetch-time 404 that previously resulted; native non-GitHub support is tracked separately. (#1034, closes #1027)
 - Regression tests for `apm compile` placement of narrow `applyTo` patterns: instructions whose matches all live deep inside one subtree are now pinned to the deepest covering directory instead of being hoisted to the project root, across both selective and single-point placement strategies. Also covers the file-walk cache that skips repeated filesystem scans for the same glob. (#871)
 - **`apm pack` marketplace builder hardening.** Local source paths are now emitted relative to `metadata.pluginRoot` (fixes double-prefix bug). New pass-through fields: `author`, `license`, `repository`, `keywords` (alias for `tags`). Curator-wins override semantics for `description`/`version` on remote entries. Security guards reject path traversal and absolute paths post-subtraction. (#1061)
@@ -24,6 +25,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- `apm compile --dry-run -t copilot` now faithfully simulates the hand-authored file guard: a `.github/copilot-instructions.md` lacking the APM marker is reported as `skipped=1` (matching the real run) instead of as `generated=1`. Previously dry-run would claim a write that a real run would refuse, giving CI preview gates a false signal. (#1048)
+- `apm compile -t claude,copilot` (and any multi-target list including `copilot`) now correctly generates `.github/copilot-instructions.md`; previously it was silently skipped on the multi-target code path. (#1048)
+- `apm compile` no longer overwrites a hand-authored `.github/copilot-instructions.md`; if the file lacks the APM-generated marker, regeneration is skipped with a warning that names the literal marker line (`<!-- Generated by APM CLI from .apm/ primitives -->`) so users can self-serve recovery. **Migration:** to adopt APM management of an existing file, either delete or rename it and re-run `apm compile`, or prepend the marker line to the top of the file and re-run `apm compile`. (#1048)
+- Generated footer in `.github/copilot-instructions.md` now reads `apm compile` (was `specify apm compile`). (#1048)
+- `apm compile --targets claude` no longer lists `@apm_modules/{owner}/{package}/CLAUDE.md` dependencies for packages that don't have a `CLAUDE.md` file on disk (#1047)
 - **`apm prune` no longer flags directories it put there itself** -- skills installed from a subdirectory path (e.g., `owner/repo/.apm/skills/skill-name`) no longer cause the parent `owner/repo/` clone to appear as an orphan. Fixes spurious removal prompts in multi-skill and monorepo-style setups. The same fix applies to `apm deps list` and `apm compile`. A genuinely orphaned `owner/repo` package is still flagged even when a sibling subdirectory dep shares the same `owner/repo` root. No changes to `apm.yml` or the lockfile are required to benefit from this fix. (#1050)
 
 ## [0.11.0] - 2026-04-29
diff --git a/README.md b/README.md
index cb1f6d94c..d84b8bb82 100644
--- a/README.md
+++ b/README.md
@@ -53,6 +53,14 @@ apm install vercel-labs/agent-skills --skill deploy-to-vercel   # one skill, per
 
 Same install gesture. You also get a [manifest, lockfile, and reproducibility](https://microsoft.github.io/apm/reference/package-types/#skill-collection-skillsnameskillmd).
 
+**Zero-config Copilot:**
+
+```bash
+apm compile -t copilot   # writes .github/copilot-instructions.md
+```
+
+One command, no configuration -- VS Code and GitHub Copilot read the file automatically. APM dogfoods this target on its own repository.
+
 ## The three promises
 
 ### 1. Portable by manifest
diff --git a/docs/src/content/docs/enterprise/security.md b/docs/src/content/docs/enterprise/security.md
index 14698f4c6..9d649d918 100644
--- a/docs/src/content/docs/enterprise/security.md
+++ b/docs/src/content/docs/enterprise/security.md
@@ -121,7 +121,7 @@ download → scan source → block or deploy → report
 
 Content scanning extends beyond install:
 
-- **`apm compile`** scans compiled output (AGENTS.md, CLAUDE.md, commands) before writing to disk. Critical findings cause `apm compile` to exit with code 1 after writing — defense-in-depth since source files were already scanned at install, but compilation assembles content from multiple sources.
+- **`apm compile`** scans compiled output (AGENTS.md, CLAUDE.md, `.github/copilot-instructions.md`, commands) before writing to disk. Critical findings cause `apm compile` to exit with code 1 after writing — defense-in-depth since source files were already scanned at install, but compilation assembles content from multiple sources. `.github/copilot-instructions.md` is assembled from global instructions in `.apm/instructions/`, including those installed under `apm_modules/`.
 - **`apm pack`** scans files before bundling. This catches hidden characters before a package is published, preventing authors from accidentally distributing tainted content.
 - **`apm unpack`** scans bundle contents before deployment. This is a pre-deployment gate matching `apm install` — critical findings block deployment unless `--force` is used.
 
diff --git a/docs/src/content/docs/getting-started/quick-start.md b/docs/src/content/docs/getting-started/quick-start.md
index 7b772d040..ca0c780f1 100644
--- a/docs/src/content/docs/getting-started/quick-start.md
+++ b/docs/src/content/docs/getting-started/quick-start.md
@@ -113,6 +113,16 @@ dependencies:
     - microsoft/apm-sample-package#v1.0.0
 ```
 
+## Get Copilot reading your packages in under a minute
+
+Run one more command:
+
+```bash
+apm compile -t copilot
+```
+
+APM assembles every global instruction it just installed into `.github/copilot-instructions.md` -- the file VS Code and GitHub Copilot read automatically. No configuration, no extra setup; open the project in VS Code and Copilot is already grounded in your packages' standards.
+
 ## That's it
 
 Open your editor. GitHub Copilot, Claude, Cursor, and OpenCode pick up the new context immediately -- no extra configuration, no compile step, no restart. The agent now knows your project's design standards, can run your prompt templates, and follows the conventions defined in the package.
diff --git a/docs/src/content/docs/reference/cli-commands.md b/docs/src/content/docs/reference/cli-commands.md
index b960b5cf3..f8033fe67 100644
--- a/docs/src/content/docs/reference/cli-commands.md
+++ b/docs/src/content/docs/reference/cli-commands.md
@@ -1748,13 +1748,13 @@ apm compile --watch
 apm compile --watch --dry-run
 
 # Target specific agent formats
-apm compile --target vscode    # AGENTS.md + .github/ only
+apm compile --target vscode    # AGENTS.md + .github/ (incl. copilot-instructions.md)
 apm compile --target claude    # CLAUDE.md + .claude/ only
 apm compile --target opencode  # AGENTS.md + .opencode/ only
 apm compile --target all       # All formats (default)
 
 # Multiple targets (comma-separated)
-apm compile -t claude,copilot  # Both CLAUDE.md and AGENTS.md
+apm compile -t claude,copilot  # CLAUDE.md + AGENTS.md + .github/copilot-instructions.md
 
 # Compile injecting Spec Kit constitution (auto-detected)
 apm compile --with-constitution
@@ -1779,6 +1779,9 @@ apm compile --no-constitution
 **Content Scanning:**
 Compiled output is scanned for hidden Unicode characters before writing to disk. Critical findings cause `apm compile` to exit with code 1 — defense-in-depth since source files are already scanned during `apm install`.
 
+**`.github/copilot-instructions.md` generation:**
+When the resolved target is `copilot` (alias `vscode`), `all`, or any multi-target list containing `copilot`, `apm compile` assembles all *global* instructions (entries in `.apm/instructions/` without an `apply_to` field) into `.github/copilot-instructions.md` -- the file VS Code and GitHub Copilot read automatically with zero user configuration. Generated content is wrapped with an APM-only marker (literal first line: `<!-- Generated by APM CLI from .apm/ primitives -->`). Switching to a non-Copilot target (e.g. `apm compile -t claude`) cleans up the file only when the marker is present; a hand-authored `.github/copilot-instructions.md` is left untouched on both write and cleanup paths. To adopt APM management of an existing hand-authored file, delete (or rename) it and re-run `apm compile`, or prepend the marker line `<!-- Generated by APM CLI from .apm/ primitives -->` to the top of the file and re-run `apm compile`.
+
 **Configuration Integration:**
 The compile command supports configuration via `apm.yml`:
 
diff --git a/src/apm_cli/commands/compile/cli.py b/src/apm_cli/commands/compile/cli.py
index 3f8fb87c7..81b040417 100644
--- a/src/apm_cli/commands/compile/cli.py
+++ b/src/apm_cli/commands/compile/cli.py
@@ -185,25 +185,47 @@ def _resolve_compile_target(target):
         return None  # will trigger detect_target() auto-detection
     if isinstance(target, list):
         target_set = set(target)
-        agents_family = {"copilot", "vscode", "agents", "cursor", "opencode", "codex"}
-        has_agents_family = bool(target_set & agents_family)
+        # Two distinct families overlap on copilot/vscode/agents:
+        #   copilot_family   -> requests .github/copilot-instructions.md AND AGENTS.md
+        #   agents_md_family -> requests AGENTS.md only (cursor/opencode/codex)
+        # Splitting these prevents the over-fire bug where -t cursor,claude or
+        # -t cursor,opencode,codex used to incorrectly emit copilot-instructions.md.
+        copilot_family = {"copilot", "vscode", "agents"}
+        agents_md_family = {"cursor", "opencode", "codex"}
+        has_copilot = bool(target_set & copilot_family)
+        has_agents_md_only = bool(target_set & agents_md_family)
         has_claude = "claude" in target_set
         has_gemini = "gemini" in target_set
         families = set()
-        if has_agents_family:
-            families.add("agents")
+        if has_copilot:
+            families.add("vscode")  # gates copilot-instructions.md
+            families.add("agents")  # also gates AGENTS.md
+        elif has_agents_md_only:
+            families.add("agents")  # AGENTS.md only -- no copilot-instructions
         if has_claude:
             families.add("claude")
         if has_gemini:
             families.add("gemini")
         if len(families) >= 2:
+            # Single-target copilot collapses {"vscode","agents"} to bare "vscode"
+            # for routing parity with single-string -t copilot.
+            if families == {"vscode", "agents"}:
+                return "vscode"
             return frozenset(families)
         elif has_claude:
             return "claude"
         elif has_gemini:
             return "gemini"
+        elif has_copilot:
+            return "vscode"
         else:
-            return "vscode"  # agents-family only
+            # cursor/opencode/codex only -- preserve the bare target name so
+            # single-element list routing matches single-string semantics
+            # (-t cursor and -t cursor both end up as "cursor").
+            for bare in ("cursor", "opencode", "codex"):
+                if bare in target_set:
+                    return bare
+            return "vscode"  # defensive fallback (unreachable)
     return target  # single string pass-through
 
 
diff --git a/src/apm_cli/compilation/agents_compiler.py b/src/apm_cli/compilation/agents_compiler.py
index 44819130d..e8ee41700 100644
--- a/src/apm_cli/compilation/agents_compiler.py
+++ b/src/apm_cli/compilation/agents_compiler.py
@@ -53,7 +53,7 @@
 # Compiler families allowed inside a multi-target frozenset (built by
 # _resolve_compile_target() from CLI-validated target names). Kept narrow
 # because the frozenset path bypasses _KNOWN_TARGETS validation.
-_KNOWN_COMPILE_FAMILIES = frozenset({"agents", "claude", "gemini"})
+_KNOWN_COMPILE_FAMILIES = frozenset({"agents", "vscode", "claude", "gemini"})
 
 
 @dataclass
@@ -883,7 +883,14 @@ def _maybe_emit_copilot_root_instructions(
         primitives: PrimitiveCollection,
         result: CompilationResult,
     ) -> CompilationResult:
-        """Generate .github/copilot-instructions.md for Copilot-capable targets."""
+        """Generate .github/copilot-instructions.md for Copilot-capable targets.
+
+        Skip semantics: if the file already exists without the APM-generated
+        marker, it is treated as hand-authored and left untouched. The
+        ``copilot_root_instructions_skipped`` stat captures this case
+        explicitly so callers can distinguish it from a genuine no-op
+        (``copilot_root_instructions_unchanged``) or an unrouted target.
+        """
         routing_target = "vscode" if config.target in _VSCODE_TARGET_ALIASES else config.target
         output_path = self.base_dir / ".github" / "copilot-instructions.md"
         if not should_compile_copilot_instructions_md(routing_target):
@@ -892,6 +899,7 @@ def _maybe_emit_copilot_root_instructions(
             result.stats.setdefault("copilot_root_instructions_generated", 0)
             result.stats.setdefault("copilot_root_instructions_written", 0)
             result.stats.setdefault("copilot_root_instructions_unchanged", 0)
+            result.stats.setdefault("copilot_root_instructions_skipped", 0)
             result.stats.setdefault("copilot_root_instructions_removed", 0)
             return result
 
@@ -905,17 +913,54 @@ def _maybe_emit_copilot_root_instructions(
             result.stats.setdefault("copilot_root_instructions_generated", 0)
             result.stats.setdefault("copilot_root_instructions_written", 0)
             result.stats.setdefault("copilot_root_instructions_unchanged", 0)
+            result.stats.setdefault("copilot_root_instructions_skipped", 0)
             result.stats.setdefault("copilot_root_instructions_removed", 0)
             return result
 
         content = self._generate_copilot_root_instructions_content(global_instructions, config)
 
         result.stats["copilot_root_instructions_generated"] = 1
+        result.stats.setdefault("copilot_root_instructions_skipped", 0)
         result.stats.setdefault("copilot_root_instructions_removed", 0)
+        result.stats.setdefault("copilot_root_instructions_written", 0)
+        result.stats.setdefault("copilot_root_instructions_unchanged", 0)
+
+        # Inspect any existing file BEFORE the dry-run early-exit so that
+        # `--dry-run` faithfully reports what a real run would do (skip vs
+        # write vs unchanged). Reading the file here is safe in dry-run mode
+        # because we never mutate it.
+        try:
+            existing = output_path.read_text(encoding="utf-8") if output_path.exists() else None
+        except OSError as exc:
+            message = f"Failed to read {output_path}: {exc}"
+            self.errors.append(message)
+            result.errors.append(message)
+            result.success = False
+            return result
+
+        if existing is not None and _COPILOT_ROOT_GENERATED_MARKER not in existing:
+            rel_path = portable_relpath(output_path, self.base_dir)
+            result.warnings.append(
+                f"Skipped {rel_path}: hand-authored file will not be overwritten. "
+                "To regenerate, either delete or rename it, or prepend the line "
+                f"'{_COPILOT_ROOT_GENERATED_MARKER}' to the top of the file. "
+                "Then re-run 'apm compile'."
+            )
+            # The file was never compared to new content; record as
+            # 'skipped', not 'unchanged'. Also reset 'generated' since no
+            # output was actually emitted (or would be, on a real run).
+            result.stats["copilot_root_instructions_generated"] = 0
+            result.stats["copilot_root_instructions_written"] = 0
+            result.stats["copilot_root_instructions_skipped"] = 1
+            result.stats["copilot_root_instructions_unchanged"] = 0
+            return result
+
+        if existing == content:
+            result.stats["copilot_root_instructions_written"] = 0
+            result.stats["copilot_root_instructions_unchanged"] = 1
+            return result
 
         if config.dry_run:
-            result.stats.setdefault("copilot_root_instructions_written", 0)
-            result.stats.setdefault("copilot_root_instructions_unchanged", 0)
             return result
 
         from ..security.gate import WARN_POLICY, SecurityGate
@@ -932,12 +977,6 @@ def _maybe_emit_copilot_root_instructions(
 
         try:
             output_path.parent.mkdir(parents=True, exist_ok=True)
-            existing = output_path.read_text(encoding="utf-8") if output_path.exists() else None
-            if existing == content:
-                result.stats["copilot_root_instructions_written"] = 0
-                result.stats["copilot_root_instructions_unchanged"] = 1
-                return result
-
             output_path.write_text(content, encoding="utf-8")
             result.stats["copilot_root_instructions_written"] = 1
             result.stats["copilot_root_instructions_unchanged"] = 0
@@ -973,7 +1012,7 @@ def _generate_copilot_root_instructions_content(
 
         sections.append("---")
         sections.append("*This file was generated by APM CLI. Do not edit manually.*")
-        sections.append("*To regenerate: `specify apm compile`*")
+        sections.append("*To regenerate: `apm compile`*")
         sections.append("")
 
         content = "\n".join(sections)
diff --git a/src/apm_cli/compilation/claude_formatter.py b/src/apm_cli/compilation/claude_formatter.py
index 945f8d215..2641cdbb8 100644
--- a/src/apm_cli/compilation/claude_formatter.py
+++ b/src/apm_cli/compilation/claude_formatter.py
@@ -212,7 +212,7 @@ def _collect_dependencies(self) -> builtins.list[str]:
         dependencies = []
         apm_modules_dir = self.base_dir / "apm_modules"
 
-        if not apm_modules_dir.exists():
+        if not apm_modules_dir.is_dir():
             return dependencies
 
         # Scan for CLAUDE.md files in apm_modules
@@ -225,6 +225,10 @@ def _collect_dependencies(self) -> builtins.list[str]:
                 if not package_dir.is_dir() or package_dir.name.startswith("."):
                     continue
 
+                claude_md_path = package_dir / "CLAUDE.md"
+                if not claude_md_path.is_file():
+                    continue
+
                 # Build the @import path
                 import_path = f"@apm_modules/{owner_dir.name}/{package_dir.name}/CLAUDE.md"
                 dependencies.append(import_path)
diff --git a/src/apm_cli/core/target_detection.py b/src/apm_cli/core/target_detection.py
index 9474e281c..6f2c977d5 100644
--- a/src/apm_cli/core/target_detection.py
+++ b/src/apm_cli/core/target_detection.py
@@ -32,7 +32,16 @@
 # Compiler families used inside a multi-target frozenset. Narrower than
 # TargetType because the families are produced by _resolve_compile_target()
 # (in the compile CLI) from CLI-validated target names.
-CompileFamily = Literal["agents", "claude", "gemini"]
+#
+# Family semantics:
+#   "agents"  -> AGENTS.md is generated (any of copilot/vscode/agents/cursor/
+#                opencode/codex was requested)
+#   "vscode"  -> .github/copilot-instructions.md is generated (only when
+#                copilot/vscode/agents was specifically requested -- NOT for
+#                cursor/opencode/codex which use their own native config files)
+#   "claude"  -> CLAUDE.md is generated
+#   "gemini"  -> GEMINI.md is generated
+CompileFamily = Literal["agents", "vscode", "claude", "gemini"]
 
 # Compile target: either a single TargetType string or a frozenset of compiler
 # families ({"agents", "claude", "gemini"}) for multi-target lists.
@@ -196,15 +205,27 @@ def should_compile_gemini_md(target: CompileTargetType) -> bool:
     return target in ("gemini", "all")
 
 
-def should_compile_copilot_instructions_md(target: TargetType) -> bool:
+def should_compile_copilot_instructions_md(target: CompileTargetType) -> bool:
     """Check if .github/copilot-instructions.md should be compiled.
 
+    Only the Copilot-native targets (copilot/vscode/agents alias) and "all"
+    trigger generation.  cursor, opencode, and codex use their own native
+    configuration files and must NOT receive copilot-instructions.md, even
+    when combined in a multi-target list.
+
     Args:
-        target: The detected or configured target
+        target: The detected or configured target. May be a string or a
+            frozenset of compiler families for multi-target lists.
 
     Returns:
         bool: True if Copilot root instructions should be generated
     """
+    if isinstance(target, frozenset):
+        # "vscode" family is added to the frozenset by _resolve_compile_target()
+        # ONLY when copilot/vscode/agents was in the original list. Checking
+        # "agents" would over-fire because cursor/opencode/codex also map to
+        # the "agents" family for AGENTS.md generation.
+        return "vscode" in target
     return target in ("vscode", "all")
 
 
diff --git a/tests/unit/compilation/test_claude_formatter.py b/tests/unit/compilation/test_claude_formatter.py
index c8265cfc7..af1363959 100644
--- a/tests/unit/compilation/test_claude_formatter.py
+++ b/tests/unit/compilation/test_claude_formatter.py
@@ -201,14 +201,27 @@ class TestDependenciesImportSyntax:
 
     @pytest.fixture
     def temp_project_with_deps(self):
-        """Create a temporary project with apm_modules dependencies."""
+        """Create a temporary project with apm_modules containing packages with and without CLAUDE.md."""
         temp_dir = tempfile.mkdtemp()
         temp_path = Path(temp_dir).resolve()
 
         # Create apm_modules structure
         apm_modules = temp_path / "apm_modules"
+        # Packages WITH CLAUDE.md - should be included
         (apm_modules / "owner1" / "package1").mkdir(parents=True)
+        (apm_modules / "owner1" / "package1" / "CLAUDE.md").write_text(
+            "# Package 1", encoding="utf-8"
+        )
         (apm_modules / "owner2" / "package2").mkdir(parents=True)
+        (apm_modules / "owner2" / "package2" / "CLAUDE.md").write_text(
+            "# Package 2", encoding="utf-8"
+        )
+        # Packages WITHOUT CLAUDE.md - should be excluded
+        (apm_modules / "owner1" / "no-claude").mkdir(parents=True)
+        (apm_modules / "owner1" / "no-claude" / "README.md").write_text(
+            "# No Claude", encoding="utf-8"
+        )
+        (apm_modules / "owner3" / "skills-only").mkdir(parents=True)
 
         yield temp_path
         shutil.rmtree(temp_dir, ignore_errors=True)
@@ -254,6 +267,14 @@ def test_no_dependencies_section_when_no_apm_modules(self, tmp_path):
 
         assert deps == []
 
+    def test_skips_packages_without_claude_md(self, temp_project_with_deps):
+        """Test that packages without a CLAUDE.md file are not listed as dependencies."""
+        formatter = ClaudeFormatter(str(temp_project_with_deps))
+        deps = formatter._collect_dependencies()
+
+        assert "@apm_modules/owner1/no-claude/CLAUDE.md" not in deps
+        assert "@apm_modules/owner3/skills-only/CLAUDE.md" not in deps
+
 
 class TestAgentsExcludedFromClaudeMd:
     """Tests verifying agents/workflows are NOT included in CLAUDE.md.
diff --git a/tests/unit/compilation/test_compile_target_flag.py b/tests/unit/compilation/test_compile_target_flag.py
index 9a738e49b..c3525d2d1 100644
--- a/tests/unit/compilation/test_compile_target_flag.py
+++ b/tests/unit/compilation/test_compile_target_flag.py
@@ -380,6 +380,313 @@ def test_cleanup_preserves_unmanaged_manual_copilot_root_instructions(self, temp
         assert root_file.read_text(encoding="utf-8") == "Manual instructions\n"
         assert result.stats["copilot_root_instructions_removed"] == 0
 
+    def test_write_path_preserves_unmanaged_manual_copilot_root_instructions(self, temp_project):
+        """Write path must not overwrite a hand-authored copilot-instructions.md.
+
+        Regression for the missing marker guard on the write path: a manually
+        authored .github/copilot-instructions.md must survive the first
+        `apm compile -t copilot` even when global instructions exist.
+        """
+        root_file = temp_project / ".github" / "copilot-instructions.md"
+        root_file.parent.mkdir(parents=True)
+        manual_content = "# Manual\n\nHand-authored guidance.\n"
+        root_file.write_text(manual_content, encoding="utf-8")
+
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing\n\nRun focused tests first.",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        result = compiler.compile(
+            CompilationConfig(target="vscode", dry_run=False, single_agents=True),
+            primitives,
+        )
+
+        assert result.success
+        assert root_file.read_text(encoding="utf-8") == manual_content
+        assert result.stats["copilot_root_instructions_written"] == 0
+        assert any("hand-authored file will not be overwritten" in w for w in result.warnings)
+        assert any(
+            "<!-- Generated by APM CLI from .apm/ primitives -->" in w for w in result.warnings
+        ), "warning must disclose the literal marker string for self-service recovery"
+
+    def test_multi_target_claude_copilot_emits_copilot_root_instructions(self, temp_project):
+        """`apm compile -t claude,copilot` (frozenset path) must emit copilot-instructions.md.
+
+        Regression for the multi-target frozenset gap: should_compile_copilot_instructions_md
+        used to ignore the frozenset branch and silently skip generation.
+        """
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing\n\nRun focused tests first.",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        result = compiler.compile(
+            CompilationConfig(
+                target=frozenset({"vscode", "agents", "claude"}),
+                dry_run=False,
+                single_agents=True,
+            ),
+            primitives,
+        )
+
+        assert result.success
+        root_file = temp_project / ".github" / "copilot-instructions.md"
+        assert root_file.exists(), (
+            "copilot-instructions.md should be generated when 'vscode' is in the frozenset target"
+        )
+        assert result.stats["copilot_root_instructions_generated"] == 1
+
+    def test_frozenset_cursor_opencode_codex_does_not_emit_copilot_instructions(self, temp_project):
+        """Round-3 regression: -t cursor,opencode,codex (no copilot family)
+        must NOT emit .github/copilot-instructions.md.
+
+        Previously the 'agents' family token was overloaded for AGENTS.md AND
+        copilot-instructions.md routing, causing the multi-target path to
+        over-fire for AGENTS.md-only combos.
+        """
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing\n\nRun focused tests first.",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        # Simulate what _resolve_compile_target(["cursor","opencode","codex"]) returns
+        # under the new semantics: a single 'agents'-only family collapses to
+        # the bare cursor target, which routes correctly via the string path.
+        result = compiler.compile(
+            CompilationConfig(target="cursor", dry_run=False, single_agents=True),
+            primitives,
+        )
+
+        assert result.success
+        root_file = temp_project / ".github" / "copilot-instructions.md"
+        assert not root_file.exists(), (
+            "copilot-instructions.md must NOT be generated for cursor/opencode/codex"
+        )
+        assert result.stats.get("copilot_root_instructions_generated", 0) == 0
+
+    def test_resolve_compile_target_cursor_opencode_codex_does_not_route_to_vscode(self):
+        """Round-3 regression at the resolver: cursor/opencode/codex multi-target
+        list must not collapse to 'vscode' (which would wrongly route
+        copilot-instructions.md generation)."""
+        from apm_cli.commands.compile.cli import _resolve_compile_target
+        from apm_cli.core.target_detection import should_compile_copilot_instructions_md
+
+        for target_list in (
+            ["cursor"],
+            ["opencode"],
+            ["codex"],
+            ["cursor", "opencode"],
+            ["cursor", "opencode", "codex"],
+        ):
+            resolved = _resolve_compile_target(target_list)
+            assert resolved != "vscode", (
+                f"_resolve_compile_target({target_list!r}) must not return 'vscode' "
+                f"-- got {resolved!r}"
+            )
+            assert should_compile_copilot_instructions_md(resolved) is False, (
+                f"copilot-instructions.md must not be routed for {target_list!r}"
+            )
+
+    def test_resolve_compile_target_copilot_family_combos_do_route(self):
+        """Cross-check: copilot-family multi-target combos still route to
+        copilot-instructions.md generation under the new predicate."""
+        from apm_cli.commands.compile.cli import _resolve_compile_target
+        from apm_cli.core.target_detection import should_compile_copilot_instructions_md
+
+        for target_list in (
+            ["copilot"],
+            ["vscode"],
+            ["claude", "copilot"],
+            ["claude", "vscode"],
+            ["gemini", "vscode"],
+            ["cursor", "vscode"],
+            ["claude", "vscode", "gemini"],
+        ):
+            resolved = _resolve_compile_target(target_list)
+            assert should_compile_copilot_instructions_md(resolved) is True, (
+                f"copilot-instructions.md must be routed for {target_list!r} "
+                f"-- resolver returned {resolved!r}"
+            )
+
+    def test_skipped_hand_authored_file_records_skipped_stat_not_unchanged(self, temp_project):
+        """Round-3 regression: the skip-on-hand-authored-file path must record
+        'skipped' in stats and reset 'generated' to 0, not leave it at 1
+        (false positive) or use 'unchanged' (semantically wrong)."""
+        root_file = temp_project / ".github" / "copilot-instructions.md"
+        root_file.parent.mkdir(parents=True)
+        root_file.write_text("# Hand-authored\n", encoding="utf-8")
+
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing\n\nRun focused tests first.",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        result = compiler.compile(
+            CompilationConfig(target="vscode", dry_run=False, single_agents=True),
+            primitives,
+        )
+
+        assert result.success
+        assert result.stats["copilot_root_instructions_generated"] == 0, (
+            "generated must be 0 when the hand-authored guard fires (no file was emitted)"
+        )
+        assert result.stats["copilot_root_instructions_written"] == 0
+        assert result.stats["copilot_root_instructions_skipped"] == 1, (
+            "skipped stat must be 1 to distinguish from a genuine no-op"
+        )
+        assert result.stats["copilot_root_instructions_unchanged"] == 0, (
+            "unchanged means content was compared and matched -- not the case here"
+        )
+
+    def test_skip_warning_uses_relative_path_and_concrete_action(self, temp_project):
+        """Round-3 UX fix: warning must use a relative path and tell the user
+        exactly what command to run after removing the file."""
+        root_file = temp_project / ".github" / "copilot-instructions.md"
+        root_file.parent.mkdir(parents=True)
+        root_file.write_text("# Hand-authored\n", encoding="utf-8")
+
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing\n\nRun focused tests first.",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        result = compiler.compile(
+            CompilationConfig(target="vscode", dry_run=False, single_agents=True),
+            primitives,
+        )
+
+        skip_warnings = [
+            w for w in result.warnings if "hand-authored file will not be overwritten" in w
+        ]
+        assert skip_warnings, "expected a skip warning to be emitted"
+        warning = skip_warnings[0]
+        assert ".github/copilot-instructions.md" in warning, "warning must reference the file"
+        assert str(temp_project) not in warning, (
+            "warning must not embed the absolute project path (use a relative path)"
+        )
+        assert "apm compile" in warning, "warning must tell the user the next command to run"
+        assert "delete or rename" in warning, "warning must give a concrete action"
+        assert "<!-- Generated by APM CLI from .apm/ primitives -->" in warning, (
+            "warning must disclose the literal marker string so users can self-serve recovery"
+        )
+
+    def test_dry_run_respects_hand_authored_guard(self, temp_project):
+        """Round-4 regression: `--dry-run` must mirror the hand-authored guard
+        the real run applies, not silently report `generated=1` for a file the
+        real run would skip. CI scripts that use `--dry-run` as a preview gate
+        depend on the simulation being faithful."""
+        root_file = temp_project / ".github" / "copilot-instructions.md"
+        root_file.parent.mkdir(parents=True)
+        manual_content = "# Hand-authored\n\nNo APM marker present.\n"
+        root_file.write_text(manual_content, encoding="utf-8")
+
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing\n\nRun focused tests first.",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        result = compiler.compile(
+            CompilationConfig(target="vscode", dry_run=True, single_agents=True),
+            primitives,
+        )
+
+        assert result.success
+        # Dry-run must not mutate the file.
+        assert root_file.read_text(encoding="utf-8") == manual_content
+        # Stats must mirror what a real run would record.
+        assert result.stats["copilot_root_instructions_generated"] == 0, (
+            "dry-run must not claim generation when the real run would skip"
+        )
+        assert result.stats["copilot_root_instructions_written"] == 0
+        assert result.stats["copilot_root_instructions_skipped"] == 1, (
+            "dry-run must surface the skip the real run would record"
+        )
+        assert result.stats["copilot_root_instructions_unchanged"] == 0
+        assert any(
+            "hand-authored file will not be overwritten" in w for w in result.warnings
+        ), "dry-run must surface the same warning a real run would emit"
+
+    def test_generated_footer_uses_apm_compile_not_specify(self, temp_project):
+        """Generated footer must read `apm compile`, not `specify apm compile`."""
+        primitives = PrimitiveCollection()
+        primitives.add_primitive(
+            Instruction(
+                name="contributing",
+                file_path=temp_project / ".apm/instructions/contributing.instructions.md",
+                description="General contributing guidance",
+                apply_to="",
+                content="# Contributing",
+                author="test",
+                source="local",
+            )
+        )
+
+        compiler = AgentsCompiler(str(temp_project))
+        result = compiler.compile(
+            CompilationConfig(target="vscode", dry_run=False, single_agents=True),
+            primitives,
+        )
+        assert result.success
+
+        content = (temp_project / ".github" / "copilot-instructions.md").read_text(encoding="utf-8")
+        assert "specify apm compile" not in content
+        assert "*To regenerate: `apm compile`*" in content
+
     def test_unknown_target_returns_failure(self, temp_project, sample_primitives):
         """Unknown target must fail explicitly instead of silently succeeding."""
         config = CompilationConfig(
@@ -1187,11 +1494,17 @@ def test_single_string_passthrough(self):
         assert _resolve_compile_target("all") == "all"
         assert _resolve_compile_target("copilot") == "copilot"
 
-    def test_list_claude_and_copilot_returns_agents_claude_set(self):
+    def test_list_claude_and_copilot_returns_full_set(self):
         from apm_cli.commands.compile.cli import _resolve_compile_target
 
-        assert _resolve_compile_target(["claude", "vscode"]) == frozenset({"agents", "claude"})
-        assert _resolve_compile_target(["claude", "copilot"]) == frozenset({"agents", "claude"})
+        # 'vscode' family member is added because copilot/vscode/agents triggers
+        # copilot-instructions.md generation; 'agents' covers AGENTS.md.
+        assert _resolve_compile_target(["claude", "vscode"]) == frozenset(
+            {"vscode", "agents", "claude"}
+        )
+        assert _resolve_compile_target(["claude", "copilot"]) == frozenset(
+            {"vscode", "agents", "claude"}
+        )
 
     def test_list_claude_only_returns_claude(self):
         from apm_cli.commands.compile.cli import _resolve_compile_target
@@ -1204,18 +1517,25 @@ def test_list_copilot_only_returns_vscode(self):
         assert _resolve_compile_target(["vscode"]) == "vscode"
         assert _resolve_compile_target(["copilot"]) == "vscode"
 
-    def test_list_agents_family_without_claude_returns_vscode(self):
-        """Targets that produce AGENTS.md but not CLAUDE.md."""
+    def test_list_agents_md_only_family_preserves_bare_target(self):
+        """cursor/opencode/codex must NOT collapse to 'vscode' (which would
+        wrongly route copilot-instructions.md). Single-element lists keep the
+        bare target name; multi-element lists pick the first present."""
         from apm_cli.commands.compile.cli import _resolve_compile_target
 
-        assert _resolve_compile_target(["cursor"]) == "vscode"
-        assert _resolve_compile_target(["opencode"]) == "vscode"
-        assert _resolve_compile_target(["codex"]) == "vscode"
-        assert _resolve_compile_target(["cursor", "opencode"]) == "vscode"
+        assert _resolve_compile_target(["cursor"]) == "cursor"
+        assert _resolve_compile_target(["opencode"]) == "opencode"
+        assert _resolve_compile_target(["codex"]) == "codex"
+        # Multi-element AGENTS.md-only list collapses to a representative bare
+        # target (cursor wins by deterministic ordering).
+        assert _resolve_compile_target(["cursor", "opencode"]) == "cursor"
+        assert _resolve_compile_target(["opencode", "codex"]) == "opencode"
 
     def test_list_cursor_and_claude_returns_agents_claude_set(self):
         from apm_cli.commands.compile.cli import _resolve_compile_target
 
+        # No 'vscode' family because copilot/vscode/agents was not requested;
+        # cursor/codex contribute only the 'agents' (AGENTS.md) family.
         assert _resolve_compile_target(["cursor", "claude"]) == frozenset({"agents", "claude"})
         assert _resolve_compile_target(["codex", "claude"]) == frozenset({"agents", "claude"})
 
@@ -1229,19 +1549,21 @@ def test_list_gemini_and_claude_returns_claude_gemini_set(self):
 
         assert _resolve_compile_target(["gemini", "claude"]) == frozenset({"claude", "gemini"})
 
-    def test_list_gemini_and_copilot_returns_agents_gemini_set(self):
+    def test_list_gemini_and_copilot_returns_full_set(self):
         from apm_cli.commands.compile.cli import _resolve_compile_target
 
-        assert _resolve_compile_target(["gemini", "vscode"]) == frozenset({"agents", "gemini"})
+        assert _resolve_compile_target(["gemini", "vscode"]) == frozenset(
+            {"vscode", "agents", "gemini"}
+        )
 
     def test_list_all_three_families_returns_full_set(self):
         from apm_cli.commands.compile.cli import _resolve_compile_target
 
         assert _resolve_compile_target(["claude", "vscode", "gemini"]) == frozenset(
-            {"agents", "claude", "gemini"}
+            {"vscode", "agents", "claude", "gemini"}
         )
         assert _resolve_compile_target(["claude", "vscode", "cursor"]) == frozenset(
-            {"agents", "claude"}
+            {"vscode", "agents", "claude"}
         )
 
 
diff --git a/tests/unit/core/test_target_detection.py b/tests/unit/core/test_target_detection.py
index 5df0286b2..c766274e0 100644
--- a/tests/unit/core/test_target_detection.py
+++ b/tests/unit/core/test_target_detection.py
@@ -261,6 +261,28 @@ def test_minimal_target(self):
     def test_claude_target(self):
         assert should_compile_copilot_instructions_md("claude") is False
 
+    def test_frozenset_with_vscode_returns_true(self):
+        """Multi-target lists containing 'vscode' family member must emit."""
+        assert (
+            should_compile_copilot_instructions_md(frozenset({"vscode", "agents", "claude"}))
+            is True
+        )
+
+    def test_frozenset_with_agents_only_returns_false(self):
+        """Multi-target lists that map cursor/opencode/codex to 'agents'
+        family for AGENTS.md routing must NOT trigger copilot-instructions.md.
+
+        This is the round-3 regression: previously the predicate checked
+        '"agents" in target' which over-fired on cursor/opencode/codex combos.
+        """
+        assert should_compile_copilot_instructions_md(frozenset({"agents", "claude"})) is False
+        assert should_compile_copilot_instructions_md(frozenset({"agents"})) is False
+
+    def test_frozenset_without_vscode_returns_false(self):
+        """Multi-target lists without 'vscode' family must not emit."""
+        assert should_compile_copilot_instructions_md(frozenset({"claude", "gemini"})) is False
+        assert should_compile_copilot_instructions_md(frozenset({"claude"})) is False
+
 
 class TestGetTargetDescription:
     """Tests for get_target_description function."""