refactor(memory): dedupe atomic-file-replace helpers across two state stores

[cyberlife-coder]

⚠️ Target branch (Git Flow)

refactor/* → targets develop. ✅

Description

Routine code-quality pass, found while looking for duplication candidates. mutation::controller::state and online_migration::job_state each carried an identical copy of the same five functions: a symlink-rejecting directory check, a symlink-rejecting regular-file check, an existence probe, and the platform-specific promote/sync_directory pair backing their staged-write-then-rename persistence.

This isn't cosmetic: it's the TOCTOU-safe symlink rejection (symlink_metadata + explicit is_symlink() reject) and the crash-safe atomic promote that the staged-write-then-promote scheme depends on in both stores. Two independent copies mean a future correctness fix to the symlink check, or a platform fix to promote/sync_directory, can land in one copy and silently miss the other.

Moved the five functions into a new shared crate::mutation::atomic_file module and updated both call sites to use it. The two message-bearing checks (validate_workspace, validate_regular_file) now take an entity: &str argument so every existing error string is reproduced byte-for-byte. The one exception: the "replacement unsupported" message on the #[cfg(not(any(unix, windows)))] branch already read three different ways across this crate (this pair plus mutation::journal::platform's own copy) for a branch that's unreachable on any platform this project ships for or runs CI on — unified to one wording rather than picking one of the three to keep arbitrarily.

Fixes # (none — proactive quality pass, no tracked issue)

Type of Change

• 🔧 Refactoring (no functional changes)

How Has This Been Tested?

• Unit tests
• cargo check -p velesdb-memory (default features, and --features persistence)
• cargo clippy -p velesdb-memory --all-targets -- -D warnings -D clippy::pedantic (clean)
• cargo test -p velesdb-memory --lib --features persistence -- --test-threads=1 (817 passed, 0 failed, 9 ignored)
• cargo fmt --all -- --check (clean)
• python3 scripts/check_prod_unwraps.py / check-todo-annotations.py (clean; unaffected by this diff, re-verified anyway)

Test Configuration:

• OS: Linux
• Rust version: per rust-toolchain.toml (MSRV 1.90)

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas — not applicable, no new logic beyond the module doc comment
• I have made corresponding changes to the documentation — not applicable, no public API or doc changes
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works — not applicable, behavior-preserving refactor already covered by existing tests
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published — not applicable

Unsafe Code Checklist

Not applicable — no unsafe code touched.

High-Risk Change Checklist

Not applicable — doesn't touch hnsw, storage, Drop, unsafe, or SIMD dispatch paths.

Additional Notes

The same five-function shape is duplicated a few more times in this crate (e.g. mutation/journal.rs's own validate_workspace/validate_regular_file, plus similar patterns in online_migration/cleanup.rs and mcp/extraction_job_store.rs). Left untouched here to keep this PR mechanical, single-purpose and reviewable; a follow-up could migrate those call sites onto crate::mutation::atomic_file too.

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics -17 complexity

Metric	Results
Complexity	-17

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