Maintain dependencies and workspace lint coverage

[isPANN]

Summary

• Update dependency minimum versions, including rmcp 3.4.0 and syn 3.0.6, with internal MCP and macro adaptations.
• Remove unused ordered-float and direct CLI tracing dependencies; narrow Tokio to rt-multi-thread.
• Exercise MCP tools, prompts, and errors over stdio.
• Run CI and make clippy across every workspace crate, target, and feature.
• Enforce the 95% coverage target without a tolerance allowance and clarify the final hung-test timeout.
• Preserve public solver/reduction APIs and mathematical semantics; 12 files, based on main.

Verification

• Integrated with all extracted safe-change branches: 6,572 workspace all-feature tests passed, 2 ignored.
• Combined changed-line Rust coverage: 99.64%.
• Workspace all-target all-feature Clippy, formatting, and whitespace checks pass.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.93%. Comparing base (7dd5fcd) to head (95c9315).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1163   +/-   ##
=======================================
  Coverage   95.93%   95.93%           
=======================================
  Files        1074     1074           
  Lines      132106   132106           
=======================================
  Hits       126730   126730           
  Misses       5376     5376           

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[GiggleLiu]

Follow-up items (recorded during final review):

• The MCP stdio integration tests (problemreductions-cli/tests/mcp_integration.rs) are gated on the mcp feature, and the CI test job runs with FEATURES=example-db, so CI only compiles them (via the new --all-features clippy) but never runs them. Consider adding make mcp-test to CI.

[GiggleLiu]

Final review: make check and make mcp-test pass locally on the merged state (main re-merged after #1155/#1156). Approving.