Migrate AGENTS maps to semantic anchors

Context

Epic #11558 migrates live instruction substrate away from positional §N references. The AGENTS.md / AGENTS_ATLAS.md pair is the core turn-loaded map and atlas substrate, so this partition should happen separately from skill and ADR/documentation migrations.

The Problem

AGENTS.md and AGENTS_ATLAS.md currently contain fragmented section numbering and cross-file §N references. This creates recurring LLM parsing cost and makes instruction identity depend on compaction-sensitive positions.

The Architectural Reality

AGENTS.md is turn-loaded memory; AGENTS_ATLAS.md carries detailed expansion. Discussion #11557 v5 selected semantic anchors as the stable identity primitive. This ticket touches high-blast instruction substrate and must follow the new ADR from #11559 plus the lint guard from #11560 once available.

The Fix

Add stable semantic anchors to AGENTS.md and AGENTS_ATLAS.md and migrate live cross-references between these files away from positional §N references.

Expected scope:

• AGENTS.md
• learn/agentos/AGENTS_ATLAS.md
• references from startup or nearby agent docs only if they point into AGENTS/ATLAS live sections

Discussion Criteria Mapping

• OQ3 Atlas numbering audit -> AGENTS_ATLAS.md included in migration scope.
• OQ4 semantic stability -> use stable explicit IDs, not volatile raw heading text.
• Step 2.5 consumer sweep -> preserve human and agent readability.
• Active/archive boundary -> live instruction refs migrate; historical references stay intentional.

Acceptance Criteria

• AGENTS.md live sections expose stable semantic anchors.
• AGENTS_ATLAS.md live sections expose stable semantic anchors.
• Live cross-references between AGENTS.md and AGENTS_ATLAS.md use semantic anchors rather than positional §N identity.
• Existing heading text remains readable; no unrelated rule rewrites or compaction churn.
• Any preserved positional references are explicitly classified as historical/archaeology or deferred with rationale.
• Lint evidence from #11560 is included if the lint guard has landed; otherwise PR body explains the temporary validation path.

Out of Scope

• Migrating .agents/skills/** references.
• Migrating ADR and general docs references.
• Changing the actual policy content beyond anchor/reference mechanics.

Avoided Traps / Gold Standards Rejected

• Contiguous renumbering is rejected as a temporary cosmetic repair.
• Rewriting unrelated AGENTS content to save bytes is rejected; this ticket is about anchor identity only.

Related

• Parent Epic: #11558
• Policy ADR ticket: #11559
• Lint ticket: #11560
• Discussion: #11557

Origin Session ID: 6e5b995a-c68e-4179-840c-a4cc48d449da Retrieval Hint: "AGENTS.md AGENTS_ATLAS.md semantic anchors cross references Option C #11558"