fix: close MCP toolset sessions

[pragnyanramtha]

Summary

• track MCP clients created by MCPSessionManager
• close tracked clients from MCPSessionManager.close() and remove successfully closed clients
• delegate MCPToolset.close() to its session manager
• add focused MCP session/toolset lifecycle regressions

Root cause

MCPToolset.close() was a no-op even though MCPToolset creates MCP clients when discovering tools and its MCPTool wrappers can create additional sessions when invoked. Those clients were not tracked for lifecycle cleanup, so callers had no way to release MCP transports through the toolset close path.

Validation

• npm install
• npm run build --workspace core
• npx vitest run --project unit:core core/test/tools/mcp/mcp_session_manager_test.ts core/test/tools/mcp/mcp_toolset_test.ts
• npx prettier --check core/src/tools/mcp/mcp_session_manager.ts core/src/tools/mcp/mcp_toolset.ts core/test/tools/mcp/mcp_session_manager_test.ts core/test/tools/mcp/mcp_toolset_test.ts
• npx eslint core/src/tools/mcp/mcp_session_manager.ts core/src/tools/mcp/mcp_toolset.ts core/test/tools/mcp/mcp_session_manager_test.ts core/test/tools/mcp/mcp_toolset_test.ts
• git diff --check

Note: npm install reports existing dependency audit findings (26 total: 9 low, 4 moderate, 13 high); no dependency changes are included in this PR.

[kalenkevich]

Related to: #377

[kalenkevich]

please revert that change

[kalenkevich]

Please revert the dev/src/cli_entrypoint.ts file change.

[pragnyanramtha]

Updated the branch to follow the maintainer feedback and keep the PR scoped to MCP session handling only.\n\nChanges in this push:\n- Reverted the CLI entrypoint change requested by @kalenkevich.\n- Removed the extra CLI stdin workaround as well, so the PR diff no longer touches CLI files.\n- Merged current main and resolved the remaining conflict in the MCP toolset test only.\n- Kept the remaining diff limited to MCP session manager/toolset code and tests.\n\nLocal verification:\n- git diff --check\n- git merge-tree --write-tree --messages HEAD origin/main\n- npm run build\n- npx vitest run --project unit:core core/test/tools/mcp/mcp_session_manager_test.ts core/test/tools/mcp/mcp_toolset_test.ts -> 17 passed