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

[edenfunf]

What

Fix compile path that silently skipped dependency instructions stored in
.github/instructions/ when running apm compile --target claude without
--local-only.

Why

Issue #631: scan_directory_with_source only scanned {dep}/.apm/ for
primitives. Packages that store instructions in .github/instructions/
(instead of .apm/instructions/) were completely invisible to
discover_primitives_with_dependencies. The --local-only and --validate
paths used LOCAL_PRIMITIVE_PATTERNS (which includes **/.github/instructions/)
so they worked, but the normal distributed compile path did not.

Symptoms:

• apm compile --target claude --verbose showed Instruction Processing: 0.0ms
• No CLAUDE.md was generated
• apm compile --target claude --local-only worked correctly
• apm compile --validate could find the instructions

How

Add DEPENDENCY_GITHUB_PRIMITIVE_PATTERNS (mirroring DEPENDENCY_PRIMITIVE_PATTERNS
for the .github/ directory layout) and scan {dep}/.github/ in
scan_directory_with_source alongside the existing .apm/ scan.

The original early-return guard if not apm_dir.exists(): return is replaced
by independent if apm_dir.exists(): / if github_dir.exists(): checks so
both directories are always considered regardless of which one is present.

No CLI interface changes. No architecture changes. Existing .apm/-based
packages are unaffected.

Test

• Reproduced issue apm compile --target claude silently skips dependency instructions without --local-only #631: .github/-only dependency → 0 instructions before fix
• Verified fix: .github/-only dependency → instruction found and CLAUDE.md generated
• --local-only still works correctly
• --target copilot unaffected
• --validate unaffected
• Regression tests added to TestScanDirectoryWithSource:
  • test_github_instructions_discovered_when_no_apm_dir
  • test_github_instructions_discovered_alongside_apm_dir
• All 348 existing unit tests pass

[sergio-sisternes-epam]

Nice fix — this is a real bug and the regression tests are well-targeted. The PR description is excellent too, clear reproduction and rationale.

Two requests before we can merge:

1. Reduce code duplication in scan_directory_with_source

The glob-scan-parse loop is copy-pasted for .apm/ and .github/. Consider extracting a small helper:

def _scan_patterns(base_dir: Path, patterns: Dict[str, List[str]], collection: PrimitiveCollection, source: str) -> None:
    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}")

Then the main function becomes:

if apm_dir.exists():
    _scan_patterns(apm_dir, DEPENDENCY_PRIMITIVE_PATTERNS, collection, source)
if github_dir.exists():
    _scan_patterns(github_dir, DEPENDENCY_GITHUB_PRIMITIVE_PATTERNS, collection, source)

This keeps the logic in one place for future maintenance.

2. Missing CHANGELOG entry

Please add an entry under ## [Unreleased] in CHANGELOG.md, e.g.:

### Fixed
- Fix `apm compile --target claude` silently skipping dependency instructions stored in `.github/instructions/` (#631)

Thanks for the contribution!

[edenfunf]

@sergio-sisternes-epam Thanks for the thorough review! Done — both points addressed in the latest commit (f67705d):

1. Extracted _scan_patterns() helper — the duplicated glob-scan-parse loop now lives in one place; scan_directory_with_source calls it for both .apm/ and .github/.
2. Added the ### Fixed entry under [Unreleased] in CHANGELOG.md.

All 63 unit tests still pass.

[Copilot]

Pull request overview

Fixes the dependency-scanning compile path so .github/instructions/ inside installed dependencies is discovered during normal distributed compilation (e.g., apm compile --target claude without --local-only), matching the behavior of --local-only/--validate.

Changes:

• Extend dependency primitive scanning to also inspect {dep}/.github/ (in addition to {dep}/.apm/) during discover_primitives_with_dependencies.
• Refactor dependency scanning into a shared _scan_patterns() helper to avoid duplicating the glob/parse loop.
• Add unit regression tests covering .github/instructions/ discovery for dependencies, and add a changelog entry under Unreleased/Fixed.

Show a summary per file

File	Description
src/apm_cli/primitives/discovery.py	Adds .github/ dependency scanning and refactors scanning loop into a helper.
tests/unit/primitives/test_discovery_parser.py	Adds regression tests ensuring dependency instructions in .github/instructions/ are discovered.
CHANGELOG.md	Documents the fix under ## [Unreleased] → ### Fixed.

Copilot's findings

Comments suppressed due to low confidence (1)

src/apm_cli/primitives/discovery.py:350

• Non-ASCII em dash (—) in this comment violates the repo's printable-ASCII encoding rule and can break Windows cp1252 terminals. Replace it with ASCII (e.g., "-" or "--").

    # 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).

• Files reviewed: 3/3 changed files
• Comments generated: 2

[Copilot]

Non-ASCII arrow character (→) in the docstring violates the repo's printable-ASCII encoding rule and may cause encoding errors on some Windows terminals. Replace with an ASCII equivalent like "->".

This issue also appears on line 348 of the same file.

Suggested change

	patterns (Dict[str, List[str]]): Primitive-type → glob-pattern mapping.
	patterns (Dict[str, List[str]]): Primitive-type -> glob-pattern mapping.

[Copilot]

Changelog formatting: add a blank line between the last bullet in ### Fixed and the next section header (### Changed) to match the surrounding Keep a Changelog style used elsewhere in this file.

Suggested change

	- Fix `apm compile --target claude` silently skipping dependency instructions stored in `.github/instructions/` (#631)
	- Fix `apm compile --target claude` silently skipping dependency instructions stored in `.github/instructions/` (#631)