fix(agent): P0 gap closure — AST ingest, sheaf meta, lean examples, MCP orphan recovery

[staticroostermedia-arch]

Summary

Closes the top P0 agent-harness gaps identified in the full-system audit (steps 1–4 + MCP UX). Stacks on #39.

1. AST ingest unification

• CLI + daemon AST paths use item.full_source for q encode (not embed_label)
• Store path unchanged (already correct)

2. Sheaf registration

• Add meta to PROCESS_SHEAF_SUBDIRS
• New processes/ritual/engram-working-memory.toml (Code Edit Ritual declarative)
• Fix agent_evolution.toml TOML parse (subagent = null → valid tables)

3. Examples lean contract

• spatial_geosphere_demo.py + ritual_verify.md: session_start + ack_wake_queue + context_for_edit (no watch_workspace at wake)

4. MCP orphan recovery

• scripts/engram-grok + grok-plugin-engram/bin/engram-grok: auto-remove stale ~/.engram/locks/mcp-*.lock when PID dead
• Docs updated in README + engram-mcp-health.sh

Verification

cargo test -p engram-server test_load_process_sheaf_registers_from_processes_dir  # PASS
cargo test -p engram-server ingest_ast_uses_full_source                          # PASS
cargo build -p engram-cli -p engram-server                                       # PASS
python3 -m py_compile examples/spatial_geosphere_demo.py                         # PASS

Live MCP (post-restart): read_concept for process:engram.meta.agent-evolution + process:engram.ritual.working-memory; verify_manifold_integrity 50/50 healthy.

Merge order

1. Merge feat(processes): codify full-system audit loop + harness + skill #39 (feat/full-system-audit-codify) first
2. Then rebase/retarget this PR to master if needed, or merge stacked