feat: add read-only agent-sudo topology view

[Ram9199]

Closes #112. Last in the founder-dogfood self-identity chain. Regroups inventory data into the view a confused user actually needs.

Goal: answer "What Agent_Sudo instances are guarding me right now?" and "What is not routed through Agent_Sudo?" — the exact questions from the original dogfood session.

What

agent-sudo topology (human view + --json), four flat sections:

1. CLI surfaces (your shell / terminal)
   agent-sudo  →  ~/.pyenv/versions/3.11.14   v0.5.6   (editable: /Volumes/Storage/Agent_Sudo)
   agent-sudo  →  ~/.pyenv/shims   (pyenv shim — resolves to the active pyenv version)
2. MCP clients (routed through Agent_Sudo)
   claude-desktop   v0.5.6   config/command/audit ...
   gemini / antigravity   v0.5.6   (→ ~/Developer engine)
3. Audit destinations
   ~/.agent-sudo/mcp-audit.jsonl              ←  claude-desktop
   ~/.agent-sudo/antigravity-mcp-audit.jsonl  ←  antigravity, gemini
4. Not routed through Agent_Sudo
   smithery   present, NOT configured to route through Agent_Sudo

On the dogfood machine this surfaces the original confusions directly: which copy the terminal uses, that Claude Desktop runs the /Volumes/Storage engine while Gemini/Antigravity run the ~/Developer engine, the two audit logs, and Smithery as present-but-not-routed.

Design constraints (all honored)

• Reuse inventory data: built on build_inventory(); the only inventory change is an additive ConfigRecord.audit_log field (extracted from the client's --audit-log arg).
• Read-only: no execution of discovered binaries, no auto-fix, no cleanup.
• No generic framework / no graph / no daemon: four flat sections; the unrouted set is a tiny concrete registry (Smithery), with probes injectable for tests.

Tests / validation

• New tests/test_topology.py (12 cases): CLI-surface ordering + shim flag, MCP client audit/editable-source join, audit-destination grouping, not-routed detection (present / absent / routed-name-excluded), formatter sections, audit-log arg extraction.
• Full suite: 505 passed. ruff clean.
• Docs: command_reference.md gains a topology entry + category-table row.

[Ram9199]

Verification pass (7 checks) — all pass; one improvement pushed.

1. Read-only ✅ — fingerprinted ~/.agent-sudo, all client configs, codex toml before/after topology + topology --json: zero changes. From an empty cwd, topology writes nothing (the repo's ./.agent-sudo is pre-existing/git-ignored, not created here).
2. CLI shim collapse ✅ — improved during this pass: the pyenv shim no longer renders as a second CLI row. It now collapses into the resolved pyenv-version install, marked [resolved via pyenv shim]. Standalone shim shown only when nothing else is on PATH. (commit ae63fee)
3. MCP clients ✅ — every client carries config path, command path, version, and audit destination.
4. Audit destinations ✅ — shared logs group correctly (gemini+antigravity); a config with no --audit-log does NOT invent a destination.
5. Not-routed ✅ — Smithery detected as present + 'NOT configured to route through Agent_Sudo'; never claims it is protected/guarded by Agent_Sudo.
6. --json == human ✅ — all four sections + the same client/audit facts present in JSON.
7. Clean machine ✅ — no clients/installs degrades gracefully: empty sections, explicit '(no …)' lines, no crash.

Full suite: 506 passed. ruff clean.