fix: scope MCP tools per turn and harden recovery paths

[alexk-dev]

Summary

• scope MCP tools to the current turn instead of mutating the global tool registry, and dedupe advertised tool definitions by name
• preserve queued internal retry messages when newer follow-ups arrive, and make session persistence/parsing failures surface instead of failing open
• add preflight dedup/schema sanitation for tool definitions before LLM request serialization, with regression tests for the new behavior

Validation

• git diff --check
• attempted targeted Maven tests, but the current workspace snapshot is missing many tracked source files outside this diff, so full compilation fails before test execution on unrelated classes (for example CommandRouter, AgentSession, ToolComponent)

[sonarqubecloud]

Quality Gate failed

Failed conditions
78.3% Coverage on New Code (required ≥ 80%)

See analysis details on SonarQube Cloud