Cleanup Memory Core 8001 substrate residuals post-ADR 0003

Context

During the resolution of the memoryCoreChroma daemon regression (#11496 / PR #11499), it was identified that while the runtime daemon and client config were fixed to respect ADR 0003 (unified Chroma on port 8000), there are still structural residuals in the ai:server-memory substrate pointing to the retired port 8001.

The Problem

The ai/mcp/server/memory-core/openapi.yaml still references http://localhost:8001 in its server URL. This is doubly wrong: it uses the retired Chroma port, and it maps the MCP transport coordinates to the database daemon coordinates. Additionally, active docs, scripts, and skills still contain obsolete instructions referencing ai:server-memory or port 8001.

The Architectural Reality

Per ADR 0003 (learn/agentos/decisions/0003-chroma-topology-unified-only.md), there is only one unified Chroma instance running on port 8000. Memory Core no longer owns a standalone Chroma daemon. Furthermore, normal MCP usage is stdio; optional HTTP/SSE uses mcpHttpPort (default 3001) via TransportService.

The Fix

1. MCP OpenAPI metadata: Do not map servers.url to Chroma 8000. Align it with the optional HTTP/SSE transport (http://localhost:3001) and describe it as optional transport metadata, or remove/neutralize the servers block entirely if stdio-only semantics are preferred.
2. Chroma/runtime operator guidance: Remove retired ai:server-memory, standalone Memory Core Chroma, and 8001 instructions from active docs/skills (e.g., .agents/skills/self-repair, .codex/HARNESS_RESTART.md, buildScripts/README.md, learn/agentos/tooling/RestorationRunbook.md, and relevant tests).
3. Historical fixtures / archived content: Do NOT rewrite generated resources/content archives or legacy backup fixtures just because they contain the number 8001. Focus only on active surfaces.

Contract Ledger Matrix

Acceptance Criteria

• ai/mcp/server/memory-core/openapi.yaml distinguishes MCP transport coordinates from database daemon coordinates (no Chroma port in the servers block).
• Active documentation, scripts, and skills are swept to remove instructions for ai:server-memory and 8001 without modifying historical fixtures or archived content.

Out of Scope

• Runtime daemon topology (already fixed in #11499).
• Modifying legacy resources/content archives or backup fixtures.

Related

• #11496 — Orchestrator still starts Memory Core Chroma after ADR 0003
• ADR 0003 — learn/agentos/decisions/0003-chroma-topology-unified-only.md

Origin Session ID: fc8abc96-ce88-407e-9d92-7fcc494f8236 Retrieval Hint: Cleanup Memory Core 8001 substrate residuals post-ADR 0003