PMAT-3954: aprender-mcp serves a caller-supplied ToolIndex; apr tools behind the default apr-tools feature

[noahgift]

Closes #3954.
keep-open: #4020 pre-existing ETXTBSY flake in a subprocess test this PR does not touch; filed separately

Why. arbiter (paiml/infra#917, ARBITER-001 row I2-2) has to serve its own MCP tools on aprender-mcp. Before this PR, AprMcpServer could serve only apr's tools:

• the dispatcher read a global index that inventory built at link time;
• initialize answered the const SERVER_NAME;
• depending on the crate linked in every apr tool plus inventory, nix, anyhow and a serde_yaml build-dependency.

What.

• ToolIndex::from_entries(Vec<(ToolDefinition, DispatchFn)>) -> Result<_, String>. Keys are owned Strings, and a duplicate name is refused.
• AprMcpServer::with_tools(name, version, Arc<ToolIndex>). initialize, tools/list, the sync call and every worker thread dispatch through the server's own index. The worker seam now takes &ToolIndex, so FALSIFY-MCP-DRAIN-005 and default_worker_dispatch_is_the_real_tool_dispatcher still exercise the real path.
• serve_stream/run_stdio return std::io::Result, and anyhow is removed.
• New default feature apr-tools gates inventory, nix and serde_yaml (all optional now), the build.rs codegen, schemas, apr's tool modules, and their tests. apr-cli names apr-tools explicitly.
• With default-features = false, features = ["native"], the normal-dependency tree is serde and serde_json plus their own dependencies.

Design. A 3-lane plan grill (three distinct gemini models) returned 3/3 FAIL on the first plan. Every consensus finding is adopted here: the anyhow leak, the worker path bypassing the index, the &'static str key, the unconditional serde_yaml build-dependency, nix not being optional, tools/args needing to stay ungated, and test gating.

Evidence.

• RED commit: ToolIndex::from_entries and AprMcpServer::with_tools don't exist (E0599).
• FALSIFY-MCP-TOOLSET-001 (tests/falsify_toolset_generic.rs): 5/5 with and without default features. It checks that serverInfo is the caller's, tools/list is exactly the caller's tools, tools/call reaches the caller's function through the worker, an unregistered tool errors, and a duplicate name is refused.
• cargo test -p aprender-mcp: green on 4 full lib runs and the full --tests run. One ETXTBSY flake appeared on the first run; it's pre-existing and filed as falsify_2384_run_apr_executes_the_resolved_binary is flaky: ETXTBSY (Text file busy) under parallel lib tests #4020.
• cargo clippy -D warnings: clean on aprender-mcp (both feature sets, all targets) and apr-cli.
• cargo metadata --locked: rc 0 at the root and in crates/facades.

After merge: arbiter can consume this only from a published aprender-mcp. The release is the operator's.

Pmat-Ticket: PMAT-3954

🤖 Generated with Claude Code

[github-actions]

§13.11 rung 1 — quorum shadow verdict

S13-SHADOW pr=4022 head=fedb6d46022d36acbde5e2ab0e97d678aefd9bae verdict=REFUSE class=Q1 arm_rc=1

Shadow mode: this records a verdict and merges nothing. A refusal
to arm is not a block (§13 adds zero rows to §7) — the pull request is
exactly as green as it was.

[noahgift]

quorum-review (AD-04): NOT agreed (auto_merge: checked=true was_armed=false disarmed=false)

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[noahgift]

quorum-review (AD-04): three PASS — agreed (auto_merge: checked=true was_armed=false disarmed=false)

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