checkpoint: Claude Code integration + implement missing MCP var tools

Add Claude Code conductor commands, MCP server, MMA exec scripts,
and implement py_get_var_declaration / py_set_var_declaration which
were registered in dispatch and tool specs but had no function bodies.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.claude/commands/conductor-verify.md

@@ -0,0 +1,85 @@
+---
+description: Run phase completion verification — tests, coverage, checkpoint commit
+---
+
+# /conductor-verify
+
+Execute the Phase Completion Verification and Checkpointing Protocol.
+Run this when all tasks in a phase are marked `[x]`.
+
+## Protocol
+
+### 1. Announce
+Tell the user: "Phase complete. Running verification and checkpointing protocol."
+
+### 2. Verify Test Coverage for Phase
+
+Find the phase scope:
+- Read `plan.md` to find the previous phase's checkpoint SHA
+- If no previous checkpoint: scope is all changes since first commit
+- Run: `git diff --name-only {previous_checkpoint_sha} HEAD`
+- For each changed code file (exclude `.json`, `.md`, `.yaml`, `.toml`):
+  - Check if a corresponding test file exists
+  - If missing: create one (analyze existing test style first)
+
+### 3. Run Automated Tests
+
+**ANNOUNCE the exact command before running:**
+> "I will now run the automated test suite. Command: `uv run pytest --cov=. --cov-report=term-missing -x`"
+
+Execute the command.
+
+**If tests fail with large output:**
+- Pipe output to `logs/phase_verify.log`
+- Spawn Tier 4 QA for analysis:
+```powershell
+uv run python scripts\claude_mma_exec.py --role tier4-qa "Analyze test failures from logs/phase_verify.log"
+```
+- Maximum 2 fix attempts
+- If still failing: **STOP**, report to user, await guidance
+
+### 4. API Hook Verification (if applicable)
+
+If the track involves UI changes:
+- Check if GUI test hooks are available on port 8999
+- Run relevant simulation tests from `tests/visual_sim_*.py`
+- Log results
+
+### 5. Present Results and WAIT
+
+Display:
+- Test results (pass/fail count)
+- Coverage report
+- Any verification logs
+
+**PAUSE HERE.** Do NOT proceed without explicit user confirmation.
+
+### 6. Create Checkpoint Commit
+
+After user confirms:
+```powershell
+git add -A
+git commit -m "conductor(checkpoint): Checkpoint end of Phase {N} - {Phase Name}"
+```
+
+### 7. Attach Verification Report via Git Notes
+```powershell
+$sha = git log -1 --format="%H"
+git notes add -m "Phase Verification Report`nCommand: {test_command}`nResult: {pass/fail}`nCoverage: {percentage}`nConfirmed by: user" $sha
+```
+
+### 8. Update plan.md
+
+Update the phase heading to include checkpoint SHA:
+```markdown
+## Phase N: {Name} [checkpoint: {sha_7}]
+```
+Commit: `conductor(plan): Mark phase '{Phase Name}' as complete`
+
+### 9. Announce Completion
+Tell the user the phase is complete with a summary of the verification report.
+
+## Context Reset
+After phase checkpointing, treat the checkpoint as ground truth.
+Prior conversational context about implementation details can be dropped.
+The checkpoint commit and git notes preserve the audit trail.