Change Array.read Shape Argument long & Store Request Validation

[brokkoli71]

Changes

API Changes

• Changed Array.read() shape parameter from int[] to long[] for consistency with offset parameter and to support arrays with dimensions > 2GB (fixes ArrayMetadata.shape: long vs Array.read: int #29)
• Updated ArrayAccessor.withShape() and IndexingUtils methods to use long[] throughout the indexing pipeline

Critical Bug Fixes

• Fixed integer overflow in computeChunkCoords() by changing numChunks to long with validation, preventing allocation failures
• Added overflow validation in computeProjection() for all long-to-int casts with descriptive error messages to prevent silent data truncation

HTTP/S3 Store Fixes

• Fixed HTTP Range header capitalization from "Bytes=" to RFC 7233 compliant "bytes=" for compatibility with strict servers
• Added HTTP response status validation to prevent serving error pages (404/500) as valid data
• Optimized S3Store.set() to use RequestBody.fromBytes() for proper content-length specification

Security Fix

• Fixed path traversal vulnerability in FilesystemStore by validating normalized absolute paths to ensure they remain within the store root.

Performance Optimizations

• Eliminated redundant I/O in Array.read() by removing the exists() check before reading chunks. This reduces I/O operations by 50% for reads, especially benefiting network stores (HTTP/S3) by removing redundant HEAD requests. Instead rely on returned null values from store. (see "Enforced strict exception handling across all stores")
• Improved sparse shard handling in ShardingIndexedCodec by efficiently returning fill values for missing shards without unnecessary allocations or exceptions.

Exception Handling Improvements

• Enforced strict exception handling across all stores (updated FilesystemStore, HttpStore, ReadOnlyZipStore), ensuring null is returned only for missing files/keys (NoSuchFileException/404) while all other I/O errors are propagated as StoreException.
• Created StoreException class with factory methods providing rich context (store path, key, underlying cause)
• Enhanced all store implementations with detailed error messages including paths, URLs, AWS status codes
• Improved Array read/write exceptions to report specific chunk coordinates during parallel operations
• Replaced generic RuntimeException with IllegalStateException for programming errors and ZarrException for user errors