Fixes and updates for file uploads

[suu-yi]

Upload system overhaul

• Moved HTTP primitives (.make_req, .url_path, constants) from client.R to api.R
• Added direct R2/S3 presigned URL upload path alongside server-proxy uploads
• Initiate request now sends file_size_bytes; completion sends parts array (ETag + PartNumber) for R2 uploads
• Presigned URL count validated against expected chunk count
• Added .put_to_presigned_url with retry, ETag validation, and proper error classification
• Raised obs_duckdb upload limit from 100MB to 2GB; max_workers default from 4 to 6

Progress bars

• Upload progress: cli bar for sequential, progressr + handler_cli for parallel (graceful fallback to sequential when progressr not installed)
• Artifact writing: consolidated cli progress bar for vars.h5 (tracks both normalized + raw batches); cli::cli_progress_step spinner for obs.duckdb
• progressr and future added to Suggests

Preparation & metadata

• Replaced all print() calls in PrepareCyteTypeR with log_info()
• Added max_metadata_categories parameter to skip high-cardinality columns during metadata aggregation
• pcent_batch_size default raised from 2000 to 5000
• HDF5 attributes fix