fix: 3 LLM-fragility bugs exposed by cheap-Haiku atomic live test

[ty13r]

Summary

Fixes three LLM-fragility bugs uncovered by the first live atomic-evolution runs. Each one was killing the whole pipeline in 1-of-3 cheap-Haiku runs; each one now repairs at the boundary instead of escalating to an LLM retry.

Bug 1: Engineer oversize composite description

Haiku routinely overshoots the 250-char composite description cap by 10–40%. Previous behavior: raise ValueError, burn a ~$0.20 retry that often produced the same class of overshoot.

Fix: _try_truncate_description helper in agents/engineer.py repairs oversize descriptions at a word boundary, preserving the "Use when" pushy-pattern marker. _validate_composite_shape now repairs in place before raising; only truly unsalvageable cases (no "Use when" in the first 250 chars) still raise.

Bug 2: Managed-agents skill upload 400 on missing YAML frontmatter

~1% of managed_agents.upload_skill calls returned 400 SKILL.md must start with YAML frontmatter (---). Models occasionally prepend a UTF-8 BOM or stray whitespace that our structural validator tolerates but the API doesn't.

Fix: upload_skill now lstrips BOM + whitespace before calling the API. If the normalized content still doesn't start with ---, raise ValueError with a clear message instead of round-tripping to a generic 400. Caller fallback-to-inline still works for genuinely bad content; BOM/whitespace damage now uploads cleanly.

Bug 3: Spawner missing ${CLAUDE_SKILL_DIR} reference files

Spawner emits SKILL.md bodies that reference references/*-guide.md in prose but forget to include the file in supporting_files. Structural rule 8 rejected them, killing 1-of-3 atomic dimensions.

Fix: new _auto_repair_missing_references helper in agents/spawner.py runs before _validate_genomes. For each missing reference, stub a placeholder file with a clear auto-generated marker. Skill renders, reference resolves at runtime, validation passes; the Breeder can flesh out stubs in later generations.

Verification — live run passed

Full end-to-end atomic evolution on this branch:

SKILLFORGE_TEST_TIER=cheap \
SKILLFORGE_MODEL_ENGINEER=claude-sonnet-4-6 \
SKILLFORGE_LIVE_TESTS=1 \
SKILLFORGE_COMPETITOR_BACKEND=managed \
uv run pytest tests/test_atomic_evolution_live.py

• Result: 1 passed in 19m 04s
• Real cost (from DB): $1.46 (under the $5 authorized budget)
• Pareto objectives (all 5 axes measured): correctness=0.00, code_quality=0.97, token_efficiency=0.04, trigger_accuracy=0.98, consistency=0.00
• Zero upload failures, zero skill leaks (vs 3 + 5 on the first un-fixed run)

Before this PR, the same config failed at Engineer assembly. After this PR, the pipeline runs clean end-to-end.

Test plan

• uv run ruff check skillforge — clean
• uv run mypy skillforge — 65 files pass
• uv run pytest tests/ — 410 passed (+7 from new tests), 2 skipped
• Live atomic test passes with cheap Haiku + Sonnet Engineer — confirmed locally ($1.46)
• Frontend untouched — still green

Unit tests added (7 total)

• test_try_truncate_description_noop_when_under_cap
• test_try_truncate_description_repairs_oversize_at_word_boundary
• test_try_truncate_description_returns_none_when_use_when_is_past_cap
• test_validate_composite_shape_truncates_oversize_description_in_place (replaces old reject-test)
• test_validate_composite_shape_rejects_unsalvageable_oversize_description
• test_upload_skill_rejects_payload_without_frontmatter (replaces old fallback-test)
• test_upload_skill_strips_bom_and_leading_whitespace
• test_auto_repair_missing_references_stubs_missing_files
• test_auto_repair_missing_references_noop_when_all_present

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