Move TODO list to separate file and update verify command

- Extract implementation TODO from DESIGN.md to TODO.md
- Remove completed Phase 1 tasks
- Add --quick option to verify command for S3 hash checking
- Update documentation to reflect deep verification as default

DESIGN.md

@@ -354,124 +354,3 @@ func EncryptAndUploadMetadata(path string, cfg *Config, snapshotID string) error
 func RunPrune(bucket, prefix, privateKey string) error
 ```
 
----
-
-## Implementation TODO
-
-### Core Infrastructure
-1. Set up Go module and project structure
-1. Create Makefile with test, fmt, and lint targets
-1. Set up cobra CLI skeleton with all commands
-1. Implement config loading and validation from YAML
-1. Create data structures for FileInfo, ChunkInfo, BlobInfo, etc.
-
-### Local Index Database
-1. Implement SQLite schema creation and migrations
-1. Create Index type with all database operations
-1. Add transaction support and proper locking
-1. Implement file tracking (save, lookup, delete)
-1. Implement chunk tracking and deduplication
-1. Implement blob tracking and chunk-to-blob mapping
-1. Write tests for all index operations
-
-### Chunking and Hashing
-1. Implement Rabin fingerprint chunker
-1. Create streaming chunk processor
-1. Implement SHA256 hashing for chunks
-1. Add configurable chunk size parameters
-1. Write tests for chunking consistency
-
-### Compression and Encryption
-1. Implement zstd compression wrapper
-1. Integrate age encryption library
-1. Create Encryptor type for public key encryption
-1. Create Decryptor type for private key decryption
-1. Implement streaming encrypt/decrypt pipelines
-1. Write tests for compression and encryption
-
-### Blob Packing
-1. Implement BlobWriter with size limits
-1. Add chunk accumulation and flushing
-1. Create blob hash calculation
-1. Implement proper error handling and rollback
-1. Write tests for blob packing scenarios
-
-### S3 Operations
-1. Integrate MinIO client library
-1. Implement S3Client wrapper type
-1. Add multipart upload support for large blobs
-1. Implement retry logic with exponential backoff
-1. Add connection pooling and timeout handling
-1. Write tests using MinIO container
-
-### Backup Command - Basic
-1. Implement directory walking with exclusion patterns
-1. Add file change detection using index
-1. Integrate chunking pipeline for changed files
-1. Implement blob upload coordination
-1. Add progress reporting to stderr
-1. Write integration tests for backup
-
-### Snapshot Metadata
-1. Implement snapshot metadata extraction from index
-1. Create SQLite snapshot database builder
-1. Add metadata compression and encryption
-1. Implement metadata chunking for large snapshots
-1. Add hash calculation and verification
-1. Implement metadata upload to S3
-1. Write tests for metadata operations
-
-### Restore Command
-1. Implement snapshot listing and selection
-1. Add metadata download and reconstruction
-1. Implement hash verification for metadata
-1. Create file restoration logic with chunk retrieval
-1. Add blob caching for efficiency
-1. Implement proper file permissions and mtime restoration
-1. Write integration tests for restore
-
-### Prune Command
-1. Implement latest snapshot detection
-1. Add referenced blob extraction from metadata
-1. Create S3 blob listing and comparison
-1. Implement safe deletion of unreferenced blobs
-1. Add dry-run mode for safety
-1. Write tests for prune scenarios
-
-### Verify Command
-1. Implement metadata integrity checking
-1. Add blob existence verification
-1. Implement quick mode (S3 hash checking)
-1. Implement deep mode (download and verify chunks)
-1. Add detailed error reporting
-1. Write tests for verification
-
-### Fetch Command
-1. Implement single-file metadata query
-1. Add minimal blob downloading for file
-1. Create streaming file reconstruction
-1. Add support for output redirection
-1. Write tests for fetch command
-
-### Daemon Mode
-1. Implement inotify watcher for Linux
-1. Add dirty path tracking in index
-1. Create periodic full scan scheduler
-1. Implement backup interval enforcement
-1. Add proper signal handling and shutdown
-1. Write tests for daemon behavior
-
-### Cron Mode
-1. Implement silent operation mode
-1. Add proper exit codes for cron
-1. Implement lock file to prevent concurrent runs
-1. Add error summary reporting
-1. Write tests for cron mode
-
-### Finalization
-1. Add comprehensive logging throughout
-1. Implement proper error wrapping and context
-1. Add performance metrics collection
-1. Create end-to-end integration tests
-1. Write documentation and examples
-1. Set up CI/CD pipeline

TODO.md

@@ -0,0 +1,112 @@
+# Implementation TODO
+
+## Local Index Database
+1. Implement SQLite schema creation
+1. Create Index type with all database operations
+1. Add transaction support and proper locking
+1. Implement file tracking (save, lookup, delete)
+1. Implement chunk tracking and deduplication
+1. Implement blob tracking and chunk-to-blob mapping
+1. Write tests for all index operations
+
+## Chunking and Hashing
+1. Implement Rabin fingerprint chunker
+1. Create streaming chunk processor
+1. Implement SHA256 hashing for chunks
+1. Add configurable chunk size parameters
+1. Write tests for chunking consistency
+
+## Compression and Encryption
+1. Implement zstd compression wrapper
+1. Integrate age encryption library
+1. Create Encryptor type for public key encryption
+1. Create Decryptor type for private key decryption
+1. Implement streaming encrypt/decrypt pipelines
+1. Write tests for compression and encryption
+
+## Blob Packing
+1. Implement BlobWriter with size limits
+1. Add chunk accumulation and flushing
+1. Create blob hash calculation
+1. Implement proper error handling and rollback
+1. Write tests for blob packing scenarios
+
+## S3 Operations
+1. Integrate MinIO client library
+1. Implement S3Client wrapper type
+1. Add multipart upload support for large blobs
+1. Implement retry logic with exponential backoff
+1. Add connection pooling and timeout handling
+1. Write tests using MinIO container
+
+## Backup Command - Basic
+1. Implement directory walking with exclusion patterns
+1. Add file change detection using index
+1. Integrate chunking pipeline for changed files
+1. Implement blob upload coordination
+1. Add progress reporting to stderr
+1. Write integration tests for backup
+
+## Snapshot Metadata
+1. Implement snapshot metadata extraction from index
+1. Create SQLite snapshot database builder
+1. Add metadata compression and encryption
+1. Implement metadata chunking for large snapshots
+1. Add hash calculation and verification
+1. Implement metadata upload to S3
+1. Write tests for metadata operations
+
+## Restore Command
+1. Implement snapshot listing and selection
+1. Add metadata download and reconstruction
+1. Implement hash verification for metadata
+1. Create file restoration logic with chunk retrieval
+1. Add blob caching for efficiency
+1. Implement proper file permissions and mtime restoration
+1. Write integration tests for restore
+
+## Prune Command
+1. Implement latest snapshot detection
+1. Add referenced blob extraction from metadata
+1. Create S3 blob listing and comparison
+1. Implement safe deletion of unreferenced blobs
+1. Add dry-run mode for safety
+1. Write tests for prune scenarios
+
+## Verify Command
+1. Implement metadata integrity checking
+1. Add blob existence verification
+1. Implement quick mode (S3 hash checking)
+1. Implement deep mode (download and verify chunks)
+1. Add detailed error reporting
+1. Write tests for verification
+
+## Fetch Command
+1. Implement single-file metadata query
+1. Add minimal blob downloading for file
+1. Create streaming file reconstruction
+1. Add support for output redirection
+1. Write tests for fetch command
+
+## Daemon Mode
+1. Implement inotify watcher for Linux
+1. Add dirty path tracking in index
+1. Create periodic full scan scheduler
+1. Implement backup interval enforcement
+1. Add proper signal handling and shutdown
+1. Write tests for daemon behavior
+
+## Cron Mode
+1. Implement silent operation mode
+1. Add proper exit codes for cron
+1. Implement lock file to prevent concurrent runs
+1. Add error summary reporting
+1. Write tests for cron mode
+
+## Finalization
+1. Add comprehensive logging throughout
+1. Implement proper error wrapping and context
+1. Add performance metrics collection
+1. Create end-to-end integration tests
+1. Write documentation and examples
+1. Set up CI/CD pipeline