[BUG] apm compile silently drops global instructions (no applyTo) from generated AGENTS.md

[ic4-y]

Bug Description

apm compile silently omits instruction files that have no applyTo frontmatter field from the generated AGENTS.md output. The optimizer reports them as placed (rel: 100% at ./AGENTS.md), but the compiled file does not contain their content.

Environment

• APM version: 0.8.10 and 0.11.0 (pip installed)
• Python version: 3.13
• OS: Linux (NixOS)

Steps to Reproduce

# 1. Create a fresh test project
mkdir -p /tmp/apm-bug/.apm/instructions
cd /tmp/apm-bug

# 2. Write minimal apm.yml
cat > apm.yml << 'EOF'
name: test-bug
version: 1.0.0
type: hybrid
target: opencode
EOF

# 3. Create a global instruction (no applyTo)
cat > .apm/instructions/global.instructions.md << 'EOF'
---
description: Global instruction without applyTo
---

This should appear in AGENTS.md.
EOF

# 4. Create a scoped instruction (has applyTo)
cat > .apm/instructions/scoped.instructions.md << 'EOF'
---
description: Scoped instruction with applyTo
applyTo: "*.md"
---

This appears in AGENTS.md for *.md files.
EOF

# 5. Compile
apm compile -t all

Expected Behavior

AGENTS.md should contain both instructions:

• The global instruction (applied to all files)
• The scoped instruction (applied to *.md files)

Actual Behavior

$ apm compile -t all
[*] Starting context compilation...
...
Optimizing placements...

  Pattern              Source          Co…   Placement           Metrics
  ──────────────────────────────────────────────────────────────────────
  (global)             global.instr…   1/1   ./AGENTS.md         rel: 100%
  *.md                 scoped.instr…   0/1   ./AGENTS.md         rel: 0%

Generated 1 AGENTS.md file

The optimizer says the global instruction is placed at ./AGENTS.md with rel: 100%, but the actual file only contains the scoped instruction:

$ cat AGENTS.md
# AGENTS.md
<!-- Generated by APM CLI from distributed .apm/ primitives -->
<!-- Source: local -->

## Files matching `*.md`
<!-- Source: local .apm/instructions/scoped.instructions.md -->
This appears in AGENTS.md for *.md files.

The global instruction's content is completely absent.

Additional Context

• Adding applyTo: "**" to the global instruction makes it appear in the output — so the compiler can handle it, but only when an explicit pattern is present.
• This affects all targets (AGENTS.md and CLAUDE.md).
• Verified on both apm-cli 0.8.10 (nixpkgs) and 0.11.0 (pip).
• No existing issues found for this specific behavior after searching the issue tracker.

Suspected Location

Likely in the compile/optimizer logic where instructions without an applyTo pattern are classified as (global) but then dropped during file generation. The optimizer's placement matrix includes them but the actual file writer appears to skip them.

[ic4-y]

Update: Reproduced on 0.11.0 as well.

The original report was run against 0.8.10 (due to PYTHONPATH pollution from the Nix store -- see below). After unsetting PYTHONPATH to get a clean 0.11.0 run, the bug is identical.

0.11.0 output

$ apm compile -t all
...
Optimizing placements...

  Pattern              Source          Co...   Placement           Metrics
  (global)             conventions.    1/1     ./AGENTS.md         rel: 100%
  *.md                 scoped.instr.   0/1     ./AGENTS.md         rel: 0%

Generated 1 AGENTS.md file

AGENTS.md still contains only the scoped instruction. The global instruction is completely absent from the output, despite the optimizer claiming rel: 100% placement.

New in 0.11.0

The compiler now emits warnings for the missing applyTo:

[!] Warning: .apm/instructions/conventions.instructions.md: No 'applyTo' pattern
specified -- instruction will apply globally

The warning repeats 5 times (once per target: AGENTS.md, CLAUDE.md, GEMINI.md, Copilot, Claude). But the warning is misleading -- the instruction is not being applied globally. It is being silently dropped from the compiled output.

Root cause of the earlier version confusion

On NixOS, nix shell nixpkgs#uv inherits a massive PYTHONPATH from the Nix store that includes the nixpkgs apm-0.8.10 package. uvx downloads 0.11.0 to a temporary venv, but Python imports the nixpkgs 0.8.10 first because it appears earlier in sys.path. The working command is:

nix shell nixpkgs#uv -c env -u PYTHONPATH -- uvx --from apm-cli apm

Unsetting PYTHONPATH prevents the nixpkgs package from shadowing the uvx-installed version.