Fix: compilation.exclude does not filter primitive discovery by Copilot · Pull Request #477 · microsoft/apm

Copilot · 2026-03-27T11:52:05Z

Description

compilation.exclude patterns were only applied during context optimization (directory scanning/placement), not during primitive discovery. This caused .instructions.md files in excluded directories to leak into compiled output.

# apm.ymlcompilation:
exclude:
- "docs/**"

Files under docs/ were still discovered, parsed, and compiled into AGENTS.md/CLAUDE.md.

Changes:

discovery.py: Added exclude_patterns parameter to discover_primitives(), discover_primitives_with_dependencies(), and scan_local_primitives() with glob matching helpers (** support, cross-platform path normalization)
agents_compiler.py: Passes config.exclude to both discovery code paths
5 new tests covering single/multiple exclude patterns across both discovery entry points

Type of change

Bug fix
New feature
Documentation
Maintenance / refactor

Testing

Tested locally
All existing tests pass
Added tests for new functionality (if applicable)

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Agent-Logs-Url: https://github.com/microsoft/apm/sessions/6aae940e-6c6a-40f5-9f06-994570e01fa7 Co-authored-by: danielmeppiel <51440732+danielmeppiel@users.noreply.github.com>

Propagate exclude patterns from CompilationConfig to the primitive discovery phase so that .instructions.md files (and other primitives) inside excluded directories are never discovered or compiled. Fixes#464 Agent-Logs-Url: https://github.com/microsoft/apm/sessions/6aae940e-6c6a-40f5-9f06-994570e01fa7 Co-authored-by: danielmeppiel <51440732+danielmeppiel@users.noreply.github.com>

Alejandro Colomina (Coolomina) · 2026-03-30T14:14:32Z

Tested, and it works :). Thank you.

Copilot

Pull request overview

Fixes a gap where compilation.exclude patterns were only applied during context optimization, not during primitive discovery, allowing excluded .instructions.md files to be discovered and compiled.

Changes:

Thread exclude_patterns through primitive discovery entry points and apply filtering before parsing discovered files.
Propagate CompilationConfig.exclude into both discovery paths in AgentsCompiler.
Add unit tests to cover exclusion behavior for local scanning and both discovery entry points.

Show a summary per file

File	Description
uv.lock	Updates editable project version metadata to 0.8.6.
src/apm_cli/primitives/discovery.py	Adds exclude-aware discovery helpers and wires exclude filtering into discovery/scan flows.
src/apm_cli/compilation/agents_compiler.py	Passes `config.exclude` into discovery functions for both local-only and dependency-aware compilation.
tests/unit/primitives/test_discovery_parser.py	Adds tests validating exclusion behavior across discovery APIs.
tests/unit/compilation/test_agents_compiler_coverage.py	Updates mock assertion for the new discovery call signature.
CHANGELOG.md	Adds an Unreleased fix entry for exclude filtering during discovery.

Copilot's findings

Files reviewed: 5/6 changed files
Comments generated: 4

Copilot · 2026-04-06T20:20:10Z

+### Fixed
+
+- `compilation.exclude` patterns now filter primitive discovery, preventing `.instructions.md` files in excluded directories from leaking into compiled output (#464)


CHANGELOG entry ends with (#464), but this PR is #477 (per PR metadata). Keep-a-Changelog convention in this repo is one line per PR ending with the PR number; please update the reference to the correct PR number (or include the correct set if intentionally grouped).

Copilot · 2026-04-06T20:20:11Z

+ try:
+ rel_path = file_path.resolve().relative_to(base_dir.resolve())
+ except ValueError:
+ return False
+
+ rel_path_str = rel_path.as_posix()
+


_should_exclude_file() uses Path.resolve().relative_to() but only catches ValueError. On Windows (and some CI setups) resolve()/relative_to() can also raise OSError/RuntimeError (e.g., 8.3 short-name mismatches). Consider using utils.paths.portable_relpath() or expanding the exception handling so exclude filtering does not crash discovery.

Copilot · 2026-04-06T20:20:11Z

 # Find and parse files for each primitive type
 for primitive_type, patterns in LOCAL_PRIMITIVE_PATTERNS.items():
 files = find_primitive_files(base_dir, patterns)

 for file_path in files:
+ if _should_exclude_file(file_path, base_path, exclude_patterns):
+ continue


discover_primitives() is used for --local-only ("Ignore dependencies"), but it does not filter out files under apm_modules/. Because LOCAL_PRIMITIVE_PATTERNS includes recursive "/.apm/..." and "/*.instructions.md" patterns, primitives from installed dependencies can still be discovered in local-only mode. Consider applying the same apm_modules exclusion used in scan_local_primitives(), or refactoring local-only discovery to reuse scan_local_primitives().

…erage - Extract duplicated glob matcher from discovery.py and context_optimizer.py into shared src/apm_cli/utils/exclude.py - Add validate_exclude_patterns() with consecutive ** collapse and segment cap (max 5 non-consecutive) to prevent exponential recursion DoS - Cover _discover_local_skill() with exclusion filtering (was bypassed) - Add debug logging for excluded files - Add 34 tests for shared exclude util (validation, matching, DoS guard) - Add SKILL.md exclusion and DoS validation tests to discovery tests - Revert uv.lock version bump artifact - Net -160 lines from deduplication Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Initial plan * Initial plan for compilation.exclude primitive discovery fix Agent-Logs-Url: https://github.com/microsoft/apm/sessions/6aae940e-6c6a-40f5-9f06-994570e01fa7 Co-authored-by: danielmeppiel <51440732+danielmeppiel@users.noreply.github.com> * fix: compilation.exclude patterns now filter primitive discovery Propagate exclude patterns from CompilationConfig to the primitive discovery phase so that .instructions.md files (and other primitives) inside excluded directories are never discovered or compiled. Fixes#464 Agent-Logs-Url: https://github.com/microsoft/apm/sessions/6aae940e-6c6a-40f5-9f06-994570e01fa7 Co-authored-by: danielmeppiel <51440732+danielmeppiel@users.noreply.github.com> * refactor: extract shared exclude matcher, add DoS guard, complete coverage - Extract duplicated glob matcher from discovery.py and context_optimizer.py into shared src/apm_cli/utils/exclude.py - Add validate_exclude_patterns() with consecutive ** collapse and segment cap (max 5 non-consecutive) to prevent exponential recursion DoS - Cover _discover_local_skill() with exclusion filtering (was bypassed) - Add debug logging for excluded files - Add 34 tests for shared exclude util (validation, matching, DoS guard) - Add SKILL.md exclusion and DoS validation tests to discovery tests - Revert uv.lock version bump artifact - Net -160 lines from deduplication Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: danielmeppiel <51440732+danielmeppiel@users.noreply.github.com> Co-authored-by: danielmeppiel <dmeppiel@microsoft.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Initial plan
a1aaf37

CopilotAI assigned Copilot and Daniel Meppiel (danielmeppiel)Mar 27, 2026

Copilotstarted work on behalf of Daniel Meppiel (danielmeppiel)March 27, 2026 11:52 View session

CopilotAI linked an issue Mar 27, 2026 that may be closed by this pull request
[BUG] compilation.exclude does not filter primitive discovery #475
Closed

CopilotAIand others added 2 commits March 27, 2026 11:54

Initial plan for compilation.exclude primitive discovery fix
a00ca77
Agent-Logs-Url: https://github.com/microsoft/apm/sessions/6aae940e-6c6a-40f5-9f06-994570e01fa7 Co-authored-by: danielmeppiel <51440732+danielmeppiel@users.noreply.github.com>

CopilotAI changed the title ~~[WIP] Fix compilation.exclude to filter primitive discovery~~Fix: compilation.exclude does not filter primitive discoveryMar 27, 2026

Copilotfinished work on behalf of Daniel Meppiel (danielmeppiel)March 27, 2026 12:01

CopilotAI requested a review from Daniel Meppiel (danielmeppiel)March 27, 2026 12:01

Alejandro Colomina (Coolomina) mentioned this pull request Mar 29, 2026
fix: apply compilation.exclude patterns during primitive discovery #476
Closed
7 tasks

Alejandro Colomina (Coolomina) approved these changes Mar 30, 2026
View reviewed changes

Daniel Meppiel (danielmeppiel) marked this pull request as ready for review April 6, 2026 20:14

CopilotAI review requested due to automatic review settings April 6, 2026 20:14

Copilotstarted reviewing on behalf of Daniel Meppiel (danielmeppiel)April 6, 2026 20:15 View session

CopilotAI reviewed Apr 6, 2026
View reviewed changes

Daniel Meppiel (danielmeppiel)and others added 2 commits April 6, 2026 22:26

Merge branch 'main' into copilot/fix-primitive-discovery-exclusion
44ce1b6

Daniel Meppiel (danielmeppiel) merged commit 3203104 into mainApr 6, 2026
6 checks passed

Daniel Meppiel (danielmeppiel) deleted the copilot/fix-primitive-discovery-exclusion branch April 6, 2026 20:36

This was referenced Apr 6, 2026
chore: prepare v0.8.11 release #598
Merged
[docs] Update documentation for features from 2026-04-07 (v0.8.11) #620
Closed

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Fix: compilation.exclude does not filter primitive discovery - #477

Fix: compilation.exclude does not filter primitive discovery#477
Daniel Meppiel (danielmeppiel) merged 5 commits into
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copilot/fix-primitive-discovery-exclusion

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		### Fixed

		- `compilation.exclude` patterns now filter primitive discovery, preventing `.instructions.md` files in excluded directories from leaking into compiled output (#464)

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CopilotAI commented Mar 27, 2026•
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