fix: resolve mainline conflicts for checkpoint diff

[fennoai]

Requested by @phantom5099

Summary

• merge conflict changes into the checkpoint diff PR branch
• restore and guard checkpoint compatibility after upstream snapshot changes
• update affected tests and verify with gofmt and go test ./...

[codecov-commenter]

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 27.03583% with 224 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
internal/checkpoint/per_edit_snapshot.go	25.00%	191 Missing and 13 partials ⚠️
internal/runtime/run.go	0.00%	13 Missing ⚠️
internal/runtime/checkpoint_restore.go	64.70%	3 Missing and 3 partials ⚠️
internal/gateway/bootstrap.go	66.66%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!