fix: update cache in-memory state after write operations

[notJoon]

Summary

Cache set/remove/clear methods did not update in-memory state after writing to disk, causing stale reads within the same process. This PR fixes the inconsistency and adds regression tests.

Changes

• Change set, remove, clear signatures from &self to &mut self so in-memory state can be mutated
• Apply write-then-commit pattern: build new state, write to disk, update memory only on success to prevent memory/disk divergence on I/O failure
• Propagate &mut self requirement to callers in fetcher, generator, main, init, and watcher
• Add test_cache_set_visible_immediately_in_same_process and test_cache_remove_visible_immediately_in_same_process regression tests

Related Issues

None

Checklist

• cargo test --all-features passes
• cargo clippy --all-targets --all-features -- -D warnings passes
• cargo fmt --all --check passes
• Updated documentation if needed
• Added tests for new functionality

[dodok8]

As #52 is merged, it made large changes to the main branch. I recommend merge main branch again.