Summary

• replace repository export/commit use of workingCopyDiff with direct Tonel export plus Git status/commit
• write .project metadata during diff-free export so committed checkouts remain attachable
• replace branch switch/pull/checkout Iceberg diff/adopt paths with Git CLI plus direct package loading/reference updates
• keep repository operation tests aligned with the new public contract instead of Iceberg internal index state

Verification

• MCPToolRepositoryOperationTest in Pharo 13: 46 passed, 1 skipped
• MCPToolRepositoryToolsTest, MCPToolContractsTest, MCPToolStructuredOutputTest: 146 passed
• MCP-Tests: 640 passed, 1 skipped
• committed and pushed through the updated repository tool path without transport drop

Addresses #65.