fix(files): make generate export atomic at the directory level

[bug-ops]

Summary

• FileSystem::export_to_filesystem now stages the entire export tree in a sibling temporary directory and publishes it via a single atomic directory rename, instead of writing files directly into the target directory.
• A process interrupted mid-generate (e.g. killed) can no longer leave a partially written ~/.claude/servers/{id}/ directory — such as an index.ts re-exporting a tool file that was never actually written, with zero detection outside the skill code path.
• Adds a best-effort sweep of orphaned staging/displaced directories left behind by a killed prior run, so they no longer accumulate indefinitely next to the target.
• Drops ExportOptions.overwrite, which had no production callers and only complicated the staging model with subtly-different fs::copy semantics.

Closes #159

Test plan

• cargo +nightly fmt --check
• cargo +stable clippy --all-targets --all-features --workspace -- -D warnings
• cargo nextest run --all-features --workspace --no-fail-fast (729 passed)
• cargo test --doc --all-features --workspace
• RUSTDOCFLAGS="--deny rustdoc::broken_intra_doc_links" cargo doc --no-deps --workspace
• cargo bench --no-run --profile bench-fast -p mcp-execution-files
• New unit tests cover: failure leaves existing target untouched, swap-into-place replace/rollback, export to a nonexistent target directory (fresh-generation fast path), staging cleanup on publish failure, sweep of orphaned artifacts from a prior crash (target-scoped, doesn't touch other targets' artifacts)