[fix] include dependency instructions in claude compile (#631)

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Pin codex setup to `rust-v0.118.0` for security and reproducibility; update config to `wire_api = "responses"` (#663)
 - Propagate headers and environment variables through OpenCode MCP adapter with defensive copies to prevent mutation (#622)
+- Fix `apm compile --target claude` silently skipping dependency instructions stored in `.github/instructions/` (#631)
 ### Changed
 
 - `apm marketplace browse/search/add/update` now route through the registry proxy when `PROXY_REGISTRY_URL` is set; `PROXY_REGISTRY_ONLY=1` blocks direct GitHub API calls (#506)

src/apm_cli/primitives/discovery.py

@@ -55,6 +55,20 @@
     ]
 }
 
+# Dependency primitive patterns for .github directory within dependencies.
+# Some packages store primitives in .github/ instead of (or in addition to) .apm/.
+DEPENDENCY_GITHUB_PRIMITIVE_PATTERNS: Dict[str, List[str]] = {
+    'chatmode': [
+        "agents/*.agent.md",
+        "chatmodes/*.chatmode.md",
+    ],
+    'instruction': ["instructions/*.instructions.md"],
+    'context': [
+        "context/*.context.md",
+        "memory/*.memory.md",
+    ]
+}
+
 
 def discover_primitives(
     base_dir: str = ".",
@@ -297,37 +311,48 @@ def get_dependency_declaration_order(base_dir: str) -> List[str]:
         return []
 
 
-def scan_directory_with_source(directory: Path, collection: PrimitiveCollection, source: str) -> None:
-    """Scan a directory for primitives with a specific source tag.
-    
+def _scan_patterns(base_dir: Path, patterns: Dict[str, List[str]], collection: PrimitiveCollection, source: str) -> None:
+    """Glob-scan-parse loop for one base directory and one patterns dict.
+
     Args:
-        directory (Path): Directory to scan (e.g., apm_modules/package_name).
+        base_dir (Path): Directory to scan (e.g., dep/.apm or dep/.github).
+        patterns (Dict[str, List[str]]): Primitive-type → glob-pattern mapping.
         collection (PrimitiveCollection): Collection to add primitives to.
         source (str): Source identifier for discovered primitives.
     """
-    # Look for .apm directory within the dependency
-    apm_dir = directory / ".apm"
-    if not apm_dir.exists():
-        # Even without .apm, check for SKILL.md (Claude Skills support)
-        _discover_skill_in_directory(directory, collection, source)
-        return
-
-    # Find and parse files for each primitive type
-    for primitive_type, patterns in DEPENDENCY_PRIMITIVE_PATTERNS.items():
-        for pattern in patterns:
-            full_pattern = str(apm_dir / pattern)
-            matching_files = glob.glob(full_pattern, recursive=True)
-
-            for file_path_str in matching_files:
+    for _primitive_type, type_patterns in patterns.items():
+        for pattern in type_patterns:
+            for file_path_str in glob.glob(str(base_dir / pattern), recursive=True):
                 file_path = Path(file_path_str)
                 if file_path.is_file() and _is_readable(file_path):
                     try:
                         primitive = parse_primitive_file(file_path, source=source)
                         collection.add_primitive(primitive)
                     except Exception as e:
                         print(f"Warning: Failed to parse dependency primitive {file_path}: {e}")
-
-    # Also check for SKILL.md in the dependency root
+
+
+def scan_directory_with_source(directory: Path, collection: PrimitiveCollection, source: str) -> None:
+    """Scan a directory for primitives with a specific source tag.
+
+    Args:
+        directory (Path): Directory to scan (e.g., apm_modules/package_name).
+        collection (PrimitiveCollection): Collection to add primitives to.
+        source (str): Source identifier for discovered primitives.
+    """
+    # Scan .apm directory within the dependency
+    apm_dir = directory / ".apm"
+    if apm_dir.exists():
+        _scan_patterns(apm_dir, DEPENDENCY_PRIMITIVE_PATTERNS, collection, source)
+
+    # Also scan .github directory — some packages store primitives there instead of (or
+    # in addition to) .apm/.  Without this, dependency instructions in .github/instructions/
+    # are silently skipped in the normal compile path (issue #631).
+    github_dir = directory / ".github"
+    if github_dir.exists():
+        _scan_patterns(github_dir, DEPENDENCY_GITHUB_PRIMITIVE_PATTERNS, collection, source)
+
+    # Check for SKILL.md in the dependency root
     _discover_skill_in_directory(directory, collection, source)
 
 

tests/unit/primitives/test_discovery_parser.py

@@ -331,6 +331,46 @@ def test_parse_error_in_dep_primitive_warns_and_continues(self):
             self.assertIn("Warning", buf.getvalue())
         self.assertEqual(collection.count(), 0)
 
+    def test_github_instructions_discovered_when_no_apm_dir(self):
+        """Regression test for issue #631.
+
+        Dependency instructions stored in .github/instructions/ must be
+        included in compile --target claude without --local-only.
+        """
+        dep_dir = Path(self.tmp) / "chkp-roniz" / "cc-rubber-duck"
+        _write(
+            dep_dir / ".github" / "instructions" / "rubber-duck.instructions.md",
+            INSTRUCTION_CONTENT,
+        )
+        collection = PrimitiveCollection()
+        scan_directory_with_source(
+            dep_dir, collection, source="dependency:chkp-roniz/cc-rubber-duck"
+        )
+        self.assertEqual(len(collection.instructions), 1)
+        self.assertEqual(
+            collection.instructions[0].source,
+            "dependency:chkp-roniz/cc-rubber-duck",
+        )
+
+    def test_github_instructions_discovered_alongside_apm_dir(self):
+        """Regression test for issue #631.
+
+        When a dependency has both .apm/instructions/ and .github/instructions/,
+        primitives from both directories must be discovered.
+        """
+        dep_dir = Path(self.tmp) / "owner" / "mixed-pkg"
+        _write(
+            dep_dir / ".apm" / "instructions" / "from-apm.instructions.md",
+            INSTRUCTION_CONTENT,
+        )
+        _write(
+            dep_dir / ".github" / "instructions" / "from-github.instructions.md",
+            INSTRUCTION_CONTENT,
+        )
+        collection = PrimitiveCollection()
+        scan_directory_with_source(dep_dir, collection, source="dependency:owner/mixed-pkg")
+        self.assertEqual(len(collection.instructions), 2)
+
 
 class TestGetDependencyDeclarationOrder(unittest.TestCase):
     """Tests for get_dependency_declaration_order."""