Stop repo-gate tracked rewrites as retained progress

[yvette-carlisle]

Summary

• classify completed repo-gate tracked-rewrite residue as retained partial progress needing operator attention
• keep canonicalization and verification failures on automatic repair
• update prompt/docs/tests so Decodex does not infer artifact, generated, or fixture semantics

Validation

• cargo make fmt-check
• cargo test -p decodex
• cargo make check-rust
• cargo make check