chore(conformance): restore wrapper-engine cross-validation (post-#24, #27, #29, #31)

[manojp99]

Restores the conformance suite to fully green and adds fresh fixtures for the post-cleanup argv surface. Closes the structural gap that let wrapper-engine drift accumulate silently through PRs #27, #29, and #31.

Why

The conformance suite (wrappers/conformance/) cross-validates that wrapper-produced wire frames are accepted by the engine end-to-end — exactly the class of bug PR #31 just fixed. It had been in pre-existing-failure status for multiple PRs:

• PR fix(wire): align all sites to protocol 0.2.0 (--mcp-config-path, schema rename, fixture bump) #24 renamed --mcp-servers → --mcp-config-path and renamed the wire-protocol fixture initialize-with-mcpservers → initialize-with-mcp-config-path — but did not update the runners that load the fixture by name. 1 failure surfaced.
• PR feat: host config layer + drop hostCapabilities surface #27 noted it as pre-existing tech debt (out of scope).
• PR chore(cli)!: drop --mcp-config-path argv flag (subsumed by host config + env var) #29 noted it as pre-existing baseline.
• PR chore(wrappers)!: drop env-allowlist, env-extra, allow-protocol-skew from wrappers (sync with engine) #31 noted it as pre-existing baseline.

Each per-PR note was true. But the cumulative effect was that the suite designed to catch wrapper-engine surface drift was muted during the entire window in which #27, #29, and #31 introduced surface changes. PR #31 found and fixed the wrapper-engine argv mismatch (3 flags the wrappers kept emitting after #27 removed them); a green conformance suite would have caught it at #27 time.

This PR catches the conformance suite up.

What's in this PR

1. Fixture-name fix (closes the long-running baseline failure):

• wrappers/conformance/test/runner-ts.test.ts and wrappers/conformance/tests/test_runner_py.py updated to reference initialize-with-mcp-config-path (the surviving fixture name from PR fix(wire): align all sites to protocol 0.2.0 (--mcp-config-path, schema rename, fixture bump) #24).
• Side benefit: tests/test_phase_2_1_exit_gate.py had the same hardcoded stale reference. Fixed alongside, closing 1 of the 4 pre-existing engine-side failures.

2. New baseline fixture (locks in the post-cleanup wire shape):

• initialize-baseline.yaml — canonical minimum initialize + turn/submit + result/final flow with only the protocol-required params (no mcpConfigPath, no allowProtocolSkew, no hostCapabilities, no envAllowlist, no envExtra). This is the invariant the engine + wrappers must agree on after all four cleanup PRs.

3. New protocol-skew override fixture (locks in design §8 D6):

• initialize-with-protocol-skew-override.yaml — companion to version_skew.yaml's strict-refuse branch. Exercises allowProtocolSkew: true from the host-config surface (the path that subsumed the --allow-protocol-skew argv flag dropped in feat: host config layer + drop hostCapabilities surface #27).

4. Remediation-text alignment:

• version_skew.yaml referenced the old --allow-protocol-skew argv flag in its scripted remediation text. Updated to direct users at allowProtocolSkew: true in the host config file (--config).

Test results

Suite	Before this PR	After this PR
Conformance TS (npm test)	4 passed, 1 failed	7 passed, 0 failed
Conformance Py (uv run pytest)	4 passed, 1 failed	7 passed, 0 failed
Engine (uv run pytest --ignore=wrappers)	518 passed, 4 failed	519 passed, 3 failed (1 closed as side effect of fixture-name fix)
TS wrapper	63/63 ✓	63/63 ✓ (unchanged)
Python wrapper	48/48 ✓	48/48 ✓ (unchanged)

Manual smoke against all 5 removed flags: each → click UsageError, exit 2. ✓

Scope note: subprocess-level argv fixtures NOT added

The original suggestion included loud-failure argv fixtures (e.g., initialize-loud-failure-host-capabilities.yaml asserting that the engine rejects the removed flag). Intentionally not in this PR because:

1. The conformance runners (runner_ts.ts, runner_py.py) use ScriptedTransport — JSON-RPC wire-frame replay — not engine subprocess invocation.
2. The fixture loader at src/amplifier_agent_lib/protocol/conformance/loader.py requires a non-empty script of wire frames. Adding a "subprocess invocation" fixture mode would require loader machinery outside this PR's scope.
3. The argv-level loud-failure invariants are already locked in at the engine layer:
   • tests/cli/test_drop_host_capabilities.py
   • tests/cli/test_drop_mcp_config_path_flag.py
   • (plus the new wrapper-side guardrails from PR chore(wrappers)!: drop env-allowlist, env-extra, allow-protocol-skew from wrappers (sync with engine) #31)
   • All exercise the dropped flags via Click's CliRunner and assert UsageError + exit 2.

If we want subprocess-level argv coverage in the conformance suite, that's a separate "extend conformance loader to support subprocess fixture mode" PR. Tracked as a follow-up — not blocking the version-bump release.

Commits

638eff2 test(conformance): add baseline + protocol-skew-override wire-shape fixtures
ed88a8a chore(conformance): align version_skew remediation text with post-#27 host-config surface
36ba0ed fix(conformance): rename runner refs to initialize-with-mcp-config-path (post-#24)

What this means for the release story

With this PR merged, the conformance suite is genuinely green and the runners actually validate wrapper-engine surface. PRs #27, #29, #31, and #30 (skills block) are all cross-side-tested at the wire-protocol layer. Safe to proceed with coordinated version bumps and the release tags.

Followup

• Extend conformance loader to support subprocess invocation mode (would let us add argv-level loud-failure fixtures inside the conformance suite rather than in the engine-side tests).
• The 3 remaining pre-existing engine failures in tests/cli/test_mode_a_v2_envelope.py use the removed --mcp-servers flag. Independent cleanup — same upstream cause as the conformance failure this PR closed (PR fix(wire): align all sites to protocol 0.2.0 (--mcp-config-path, schema rename, fixture bump) #24's incomplete rename), but engine-layer rather than conformance-layer. Worth a small fix-up PR.