Add explicit external storage IO roots and manifests

[rsasaki0109]

Summary

• Add explicit input/output storage roots with safe relative-path resolution.
• Add SHA-256 and size file manifests plus URI receipts.
• Expose root and manifest options across the Rust CLIs and Python bindings.
• Document the external-storage workflow.

Validation

• cargo fmt --all --check
• cargo test -p spatialrust-io --all-features
• cargo test -p spatialrust --no-default-features --features mvp --bin spatialrust-mvp
• cargo test -p spatialrust --no-default-features --features streaming-cli --bin spatialrust-stream
• cargo check --manifest-path crates/spatialrust-py/Cargo.toml
• Targeted Clippy checks and git diff --check
• External-SSD streaming E2E: 3 points read/written with verified receipt and SHA-256 manifest