[codex] Replace AgentOS with repository runtime

[pcharbon70]

Summary

Implements the repository runtime replacement plan end to end. The PR replaces the jido_agent_os integration with product-owned JidoCode.Runtime containers, native Jido.Pod manager topology, runtime snapshots/restoration, product entrypoint cutover, health/telemetry, contributor documentation, and acceptance coverage.

What changed

• Added one supervised repository runtime container per ManagedRepo with capacity, pod ownership, diagnostics, telemetry, health projection, and snapshot support.
• Converted repo, coding, source graph, memory graph, and context-management pods to native Jido.Pod usage through static instance managers.
• Routed AgentWorkspace, specialist lookup, source graph, memory graph, source watching, refresh scheduling, and context-management flows through the repository runtime.
• Removed local AgentOS modules, tests, config, and the jido_agent_os dependency.
• Added focused mix runtime.verify and repository runtime migration/contributor docs.
• Added acceptance coverage for concurrent repository isolation, combined graph/memory/context/specialist topology, degraded pod health, and DateTime-safe runtime/conversation metadata normalization.

Validation

Passed:

• mix test test/jido_code/runtime/repository_runtime_test.exs
• mix runtime.verify
• mix source_graph.verify
• mix memory.verify
• mix test test/jido_code/memory_graph_test.exs test/jido_code/memory_graph_workspace_test.exs test/jido_code/memory_graph_actions_test.exs test/jido_code/memory_graph_product_service_test.exs test/jido_code/memory_graph_workflow_service_test.exs
• mix test test/jido_code/conversations_child_work_test.exs test/jido_code/context_management_test.exs test/jido_code/conversations_test.exs test/jido_code/conversations_coordinator_test.exs test/jido_code/conversations_context_compaction_test.exs test/jido_code/conversations/context_memory_test.exs
• mix test test/jido_code/runtime/repository_runtime_acceptance_test.exs test/jido_code/conversations_child_work_test.exs

Full-suite caveat:

• mix test was run and failed with 995 tests, 96 failures, 4 excluded, 16 skipped. The failures are existing broad-suite drift outside this runtime replacement scope, including removed direct resource helper calls, stale LiveView selector expectations, old memory timeout expectations, large control-plane record validation cases, legacy setup/auth helper references, and unrelated conversation/control-plane timeouts.