Refresh cache metadata after timestamp-only changes

[farhan-syah]

Timestamp-only file changes repeatedly reject the unchanged candidate and block default indexing and queries. Publication now refreshes mtime hints transactionally while preserving content identity and immutable conflict checks.

Closes #4.

Changes

• cli/src/cache/store/candidate_publication.rs: Refresh timestamp hints after immutable payload checks within the existing transaction.
• cli/src/cache/store/tests/: Cover timestamp transitions, resolver enrichment, immutable conflicts, and rollback.
• cli/src/refresh/publication_error.rs: Report bounded, escaped conflict identifiers and project-specific recovery instructions.
• cli/tests/cache_metadata_refresh.rs: Cover automatic refresh and reuse through index, symbols, status, and --trust-mtime.

Checks

Local checks pass, including 1,387 tests. Windows/macOS execution remains for CI.

cargo fmt --all --check
cargo clippy --workspace --all-targets --all-features --offline -- -D warnings
cargo test --workspace --all-features --exclude code2graph-py --exclude code2graph-node --offline
cargo doc --no-deps --all-features --offline