Feature/quarantine manager

[Jordan231111]

Description

Implemented the changes proposed in #151, mostly following the outlined function prototypes and requirements. For all the edges cases I caught them and propagated an error up to the client. I leave implementation of what to do to the CLI. A lot of the code involving permissions is very messy due to the differences between unix and windows. It might be worth looking into a more OS agnostics method to achieve what we want. In implementing this I noticed a problem with how we handle original file permissions as there was no system suggested for restoring windows file permissions which we do edit as part of making a file read only. This required me to implement a very janky system to deal with how we store permissions and should be fixed/changed in a later issue.

Related Issue

Fixes #151

Type of Change

• Bug fix
• New feature
• Refactoring / CI / Docs
• Other

How to Test

cargo test quarantine_tests

Checklist

• Code follows project style (cargo fmt + cargo clippy)
• Tests added/updated and passing (cargo test)
• Documentation updated (if applicable)

[Jordan231111]

Review verdict: Request changes.

This should not merge yet.

Blocking issues:

• The permission hardening code mutates temporary Permissions values but never applies them back to the filesystem, so the quarantine directory/file modes are not actually being tightened.
• Quarantine storage is derived only from file_name(), so two different source files with the same basename can collide in quarantine and leave multiple manifest entries pointing at the same stored path.
• The current tests stay on happy paths and do not catch either case, so the green test run is not enough evidence for this subsystem.

Please fix the storage/permission logic and add targeted regression coverage for both behaviors before merging.

[Jordan231111]

Follow-up hardening changes are now pushed to this PR.

Summary of changes:

• hardened QuarantineManager so file moves, restore/delete flows, and manifest updates stay consistent under failure paths
• switched quarantine manifest persistence to atomic temp-file replacement instead of in-place writes
• fixed non-Unix permission handling and added safer restore guards for missing parents, unknown IDs, and existing destination files
• aligned the quarantine module surface with the issue contract by exporting QuarantineManager from the module root and using delete_entry
• replaced the quarantine tests with acceptance-driven coverage for quarantine, restore, delete, persisted reloads, permission-denied behavior, duplicate quarantine rejection, and cross-device move fallback