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yams/CHANGELOG.md
Trevon add7b86b8e
 v0.4.5
2025-08-21 14:40:51 +00:00

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# Changelog
All notable changes to YAMS (Yet Another Memory System) will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [v0.4.5] - 2025-08-21
### Fixed
- **MCP Server**
- Added mutex protection to StdioTransport for thread-safe I/O operations
- Fixed potential JSON response interleaving when multiple clients connect
- Prevents "Expected ',' or ']' after array element" errors in concurrent scenarios
- Fixed missing includes for file operations
- **Test Failures**
- Fixed FilesystemBackend::list() key reconstruction from sharded paths
- Fixed ManifestManager statistics by moving static counters to member variables
- Fixed file type detection consistency in CommandIntegrationTest
- Fixed heap-use-after-free in IPC server async socket handling
- **Detection Module**
- Ensured FileSignature creation uses consistent methods for isBinary and fileType
- Fixed mismatch between FileSignature fields and classification methods
## [v0.4.4] - 2025-08-21
**CI version bump**
## [v0.4.3] - 2025-08-20
### Fixed
- **Build System**
- Updated GTest from 1.14.0 to 1.15.0 for Conan 2.0 compatibility
- **Homebrew Formula**
- Fixed documentation URL in Homebrew formula to point to correct repository
### Known Issues
- Daemon may crash when processing certain stats requests (investigation ongoing)
## [v0.4.2] - 2025-08-20
### Added
- **Linux Package Support**
- Added AppImage support for universal Linux distribution
- Integrated package building into GitHub release workflow
### Fixed
- **Linux Build Compilation**
- Fixed C++ template name lookup issues in `message_serializer.cpp` for GCC 13
- Added namespace qualification to 31 deserialize calls for proper template resolution
- Fixed missing `<utility>` header in `async_socket.h` and `connection_pool.h` for `std::exchange`
- Fixed missing `<netinet/in.h>` header in `async_socket.cpp` for `IPPROTO_TCP` constant
- **Position-Independent Code (-fPIC) Linker Errors**
- Fixed shared library linking errors by enabling PIC for all static libraries in dependency chain
- Added `POSITION_INDEPENDENT_CODE ON` property to 11 static libraries
- Resolved `yams_onnx_plugin.so` build failure on Linux x86_64
- **Missing Symbol Linker Errors**
- Fixed undefined reference to `HybridFuzzySearch` by linking `yams_metadata` to `yams::search`
- Resolved circular dependency issues in library linking order
- **CLI Output Cleanup**
- Changed TextExtractorFactory initialization logging from info to debug level
- Removed spurious log messages from normal CLI output
- **Homebrew Formula**
- Fixed documentation URL in Homebrew formula to point to correct repository
## [v0.4.1] - 2025-08-20
### Added
- **Smart Text Extraction by Default**
- CLI commands now extract text from PDFs, HTML, and other supported formats by default
- `cat` command: Shows readable text instead of binary data for PDFs and HTML files
- `get` command: Auto-detects output destination - extracts text for terminal, raw for files
- `--raw` flag added to both commands for accessing original content when needed
- `--extract` flag for `get` command to force text extraction even when piping
### Changed
- **MCP Server Text Extraction**
- Now uses `TextExtractorFactory` for all supported file types (not just HTML)
- PDF text extraction works correctly in MCP tools
- Consistent text extraction behavior across CLI and MCP interfaces
### Fixed
- **PDF Text Extraction in MCP**
- Fixed issue where PDF files returned empty content in MCP tools
- MCP server now properly extracts text from PDFs using PDFium
- Added missing `HtmlTextExtractor` to build system
- **Compilation Issues**
- Fixed missing `HtmlTextExtractor` in CMakeLists.txt
- Fixed ErrorCode enum references in HTML text extractor
- Fixed regex_replace lambda usage for C++ standard compliance
- IPC Response variant construction
- GitHub Actions release workflow: wrap embedded multi-line Python f-string code in bash here-docs and pass JSON file path via argv in the benchmarks block to avoid shell syntax errors on runners.
## [v0.4.0] - 2025-08-20
### Added
- **Universal Content Handler System**
- New `IContentHandler` interface supporting all file types with metadata extraction
- `ContentHandlerRegistry` with thread-safe handler management
- `TextContentHandler` adapter wrapping existing PlainTextExtractor
- `PdfContentHandler` wrapper for existing PdfExtractor
- `BinaryContentHandler` as universal fallback for unknown file types
- Updated DocumentIndexer to use new ContentHandlerRegistry system
- Maintained backward compatibility with legacy TextExtractor system
- **High-Performance Daemon Architecture**
- New `yams-daemon` background service for persistent resource management
- Unix domain socket IPC with zero-copy transfers for large payloads
- Automatic daemon lifecycle management with configurable policies
- `yams daemon start/stop/status/restart` command suite
- Auto-start on first command if daemon enabled in config
- Shared EmbeddingGenerator across all operations eliminates model loading overhead
- VectorIndexManager cached in daemon memory
- **Robust Downloader Module**
- New download module with libcurl adapter, repo-local staging
- SHA-256 integrity verification and rate limiting
- Atomic finalize into CAS (store-only by default)
- New `yams download` command returning JSON {hash, stored_path, size_bytes}
- Progress output (human/json) with no user-path writes unless export requested
- **Configuration v2 Architecture**
- New `[daemon]` section for service configuration
- `[daemon.models]` for model lifecycle management
- `[daemon.lifecycle]` for auto-start and shutdown policies
- `[daemon.ipc]` for communication tuning
- Backward compatible with direct mode (no daemon)
- **Enhanced Search Capabilities**
- `--literal-text` flag for search and grep commands
- Treats query patterns as literal text instead of regex/operators
- Works across all search engines (fuzzy, hybrid, metadata, vector)
- Example: `yams search "call(" --literal-text` safely searches for parentheses
### Changed
- **Performance Architecture**
- All CLI commands can leverage shared daemon resources
- Shared result renderer system across CLI and daemon
- Deferred initialization eliminates startup overhead
- **MCP Integration Improvements**
- Removed HTTP transport support, now stdio-only for cleaner local integration
- Improved EmbeddingGenerator lifecycle with lazy loading
- Better resource management with on-demand initialization
### Fixed
- **Daemon Integration Issues**
- Eliminated "Failed to preload model" warnings
- Fixed daemon configuration defaults for missing config sections
- Daemon now gracefully handles missing `[daemon]` sections in config files
- **Configuration System**
- ConfigMigrator properly handles v1 to v2 migrations without breaking existing configs
- **MCP Schema Compliance**
- Fixed "Expected object, received null" error in tool definitions
- Removed empty `properties: {}` fields from tools with no parameters
- MCP server now loads correctly without schema validation errors
- **Search Engine Robustness**
- Special characters in search queries no longer break FTS5
- Automatic sanitization prevents syntax errors from `()[]{}*"` characters
- All search paths (fuzzy, hybrid, metadata) handle special characters safely
- Raw query strings flow through pipeline unchanged until FTS5 level
- **Critical Compilation Errors**
- Fixed `ChunkingStrategy` enum reference mismatch in document chunker (FixedSize → FIXED_SIZE)
- Fixed constructor initialization order in VectorIndexOptimizer to match member declaration order
- Fixed compression level configuration in RecoveryManager (now uses level 3 per performance benchmarks)
- **Code Quality Issues**
- Fixed hundreds of uninitialized variable errors identified by cppcheck analysis
- Eliminated critical errors in recovery_manager.cpp, error_handler.cpp, and metadata_api.cpp
- Added proper RAII initialization patterns across vector and compression components
- **Build System Stability**
- All modules now compile successfully without errors
- Fixed warning configurations that were breaking dependency builds
- Improved cross-platform compilation compatibility
## [v0.3.4] - 2025-08-16
### Added
- **Hybrid Grep Command**
- Semantic search capability integrated into grep command
- Shows both "Text Matches" (regex) and "Semantic Matches" sections
- `--regex-only` flag to disable semantic search when needed
- `--semantic-limit` option to control number of semantic results (default: 3)
- Automatic parallel execution of regex and semantic searches for better performance
- **Enhanced Vector Search**
- Query embedding generation for accurate semantic search
- Automatic embedding generator creation based on available models
- Improved search accuracy with actual query vectors instead of placeholders
- Default embedding support through factory pattern
- **Automatic Embedding Generation**
- Vector database auto-creation on initialization
- Repair thread auto-starts when missing embeddings detected
- Background embedding generation without manual intervention
- Proactive database initialization to avoid "Not found" messages
### Fixed
- **Vector Database Initialization**
- Fixed auto-creation of vectors.db on first run
- Repair thread now triggers during storage initialization
- Improved embedding health detection with better sampling
- Correct variable names in initialization code (metadataRepo_ vs metadataRepository_)
### Changed
- **Search Command**
- Now uses hybrid search by default with vector and keyword fusion
- Ignores --type flag for better ergonomics (hybrid is always best)
- Automatic fallback to keyword search if vector search unavailable
## [v0.3.3] - 2025-08-15
### Added
- **MCP Server**
- Spec-compliant stdio framing (Content-Length + CRLF) with readiness notifications
- Tool schemas aligned with implementation and tests
- MCP tool handlers refactored into thin adapters that map JSON ↔ service DTOs
- CLI/MCP parity via shared service layer (Search, Grep, Document); MCP now delegates:
- grep_documents → GrepService
- list_documents, retrieve_document, update_document_metadata, get_by_name, cat_document, delete_by_name → DocumentService
- **Tracy Profiling Support**
- **List Command Enhancements**
- `--changes` flag to show documents with recent modifications (last 24h by default)
- `--since` option to show documents changed since specified time (ISO8601, relative, or natural formats)
- `--diff-tags` flag for grouped change visualization showing added/modified/deleted documents
- `--show-deleted` flag to include deleted documents in listings
- File type indicators in diff-tags output showing `[extension|bin/txt|category]` for all files
- **Grep Command Enhancements**
- Support for searching specific file paths in addition to patterns
- Improved path matching with suffix lookup for partial paths
- `--paths-only` flag for LLM-friendly output (one file path per line)
- **Code Quality**
- Added clang-format configuration for consistent code style
- Pre-commit hook for automatic code formatting
- Application services layer for shared CLI/MCP functionality
### Fixed
- **MCP Server Initialization**
- **Vector Database**: Simplified embedding generation using existing repair command patterns
- Stats no longer unconditionally recommends 'yams repair --embeddings' when embeddings already exist; guidance is shown only when count is zero
- **Stats Display**: Improved embedding system status to show meaningful health info instead of misleading zero-activity counters
- **Vector Index**: Fixed initialization with smart dimension detection from existing models and databases
- **Async Processing**: Documents now get embeddings generated asynchronously in detached threads (non-blocking)
- **Reliability**: Embedding generation now works by default, if it fails you will see ```yams repair --embeddings``` in ```yams status```
- **Stats Command**: Replaced confusing worker activity counters with clear system capability status
- **List Command Filtering**: Fixed diff-tags logic to properly skip change filters when showing diff visualization
- **Security**
- Fixed command injection vulnerability in model_command.cpp by replacing system() calls with safe execvp()
- Added path validation and sanitization for user inputs
- Validate output paths to prevent directory traversal attacks
## [v0.3.2] - 2025-08-15
### Added
- **Preview: Vector Database (experimental)**
- `SqliteVecBackend` for persistent vector storage via the sqlite-vec extension
- BLOB storage format for embeddings with transaction-safe writes across vector and metadata tables
- CLI integration: enable via `yams init` or follow prompts shown in `yams stats --health`
- **MCP Server**
- Stdio transport only; HTTP framework dependencies removed
### Fixed
- **Vector DB**
- Embeddings now persist across restarts
- Updated CRUD operations for new two-table architecture
- **Build/CI**
- Fixed Conan ARM64 architecture detection on macOS self-hosted runner
- **MCP**
- Removed Drogon and Boost dependencies that caused runtime issues
### Notes
- **Usage**
- Vector search is off by default. Initialize and configure embeddings with `yams init` or via health prompts in `yams stats --health`.
- **Requirements**
- SQLite with the sqlite-vec extension available at runtime.
- **Limitations (preview)**
- Schema and APIs may change between minor versions.
- Not enabled by default; indexing currently targets text documents only.
- Single-process/local database only; no cross-process index sharing yet.
## [v0.3.1] - 2025-08-14
### Fixed
- **Critical: Missing ref_transactions table after init**
- Fixed incomplete schema initialization in reference counter that caused "no such table: ref_transactions" error
- Added complete inline schema fallback with all required tables (ref_transactions, ref_transaction_ops, ref_statistics, ref_audit_log)
- Implemented proper resource file discovery for production deployments
- Added installation of SQL schema files to CMake configuration
- **CI/CD Workflow Simplification**
- Removed all cross-compilation logic from release workflow
- Fixed CI build failures on Linux (gtest cache corruption) and macOS (runner detection)
- Moved macOS x86_64 builds to GitHub hosted runners (macos-13)
- Docker builds now use native architecture on each runner (ARM on macOS, x86 on Linux)
### Changed
- **Build Infrastructure**
- All builds now use native compilation for better performance and reliability
- Simplified Conan configuration by removing cross-compilation complexity
- Docker workflow split into separate jobs per architecture for efficiency
- Data files (magic_numbers.json, reference_schema.sql) now properly installed with binary
## [v0.3.0] - 2025-08-14
### Added
- **Apple Silicon Optimizations**
- New `YAMS_ENABLE_APPLE_SILICON_OPTIMIZATIONS` CMake option (enabled by default on ARM64 Macs)
- Native `-mcpu=apple-m1` optimization flag for M1/M2/M3 processors
- Added `-fvectorize` for improved SIMD utilization on Apple Silicon
### Fixed
- **CI/CD C++ Standard Configuration**
- Fixed Conan profile resetting to C++17 in CI/CD workflows
- Added explicit C++20 enforcement after `conan profile detect --force`
- Fixed cross-compilation profile configurations for both CI and Release workflows
## [v0.2.9] - 2025-08-14
**Enhanced Deduplication Reporting**
- New stats --dedup command for block-level analysis
- Shows deduplication ratio, space savings, most duplicated blocks
- Validated 32% deduplication on real codebases
**CI version bump**
- Fixed CMake export error with spdlog dependency
- Resolved CI failures on macOS x64 and Linux x86
## [v0.2.8] - 2025-08-14
### Added
- **Repair Command**: New comprehensive storage maintenance command
- `yams repair --orphans`: Clean orphaned metadata entries (removed 28,101 orphaned entries in testing)
- `yams repair --chunks`: Remove orphaned chunk files (freed 38MB from 23,988 orphaned chunks)
- `yams repair --mime`: Fix missing MIME types in documents
- `yams repair --optimize`: Vacuum and optimize database (reduced 314MB to 272MB)
- `yams repair --all`: Run all repair operations
- Dry-run support with `--dry-run` flag for safe preview
- Force mode with `--force` to skip confirmations
- **Delete Command Enhancements**:
- Added `--directory` option for recursive directory deletion
- Improved metadata cleanup when deleting documents
- Added progress indicator for large deletion operations
- Properly removes both manifest and chunk files
- Fixed orphaned metadata cleanup after storage deletion
- **Config Command Enhancements**:
- Added compression tuning support via configuration
- `config get` - Retrieve configuration values
- `config set` - Set configuration values (placeholder)
- `config list` - List all configuration settings
- `config validate` - Validate configuration file
- `config export` - Export configuration in TOML or JSON format
### Fixed
- **Stats Command**:
- Fixed object file counting (was showing 0, now correctly counts chunks)
- Fixed unique document calculation to match total when no duplicates exist
- Added orphaned chunk detection and reporting
- Fixed deduplication stats to only show when duplicates exist
- Properly filters orphaned metadata entries from counts (28,101 orphaned found)
- Added chunk health reporting with progress indicator
- Fixed verbose mode not being properly tracked
- **Storage Path Issues**:
- Fixed duplicate "storage" in path construction bug throughout codebase
- Fixed content_store_impl.cpp manifest and object paths
- Fixed same issue in delete_command.cpp and repair_command.cpp
- **Chunk Management Crisis**:
- Delete command wasn't properly removing chunks when ref_count reached 0
- Implemented proper chunk cleanup when documents are deleted
- Added reference counting verification in repair command
- Fixed hash format mismatch between database (64 chars) and filesystem (62 chars + 2 char directory)
- **Database Issues**:
- Fixed view vs table issue with `unreferenced_blocks` (it's a VIEW not a table)
- Properly clean `block_references` table where `ref_count = 0`
- Added database optimization to reclaim space from deleted entries
- Database reduced from 314MB to 272MB after VACUUM
### Changed
- **Stats Output**: Improved formatting and information display
- Shows storage overhead calculation
- Displays warnings for orphaned chunks and metadata
- Only shows deduplication info when relevant
- Added database inconsistency warnings
- Better progress indicators for long operations
## [v0.2.7] - 2025-08-14
### Fixed
- **CI version bump**
- Conan flag fix in CI
## [v0.2.6] - 2025-08-14
### Fixed
- **CI version bump**
- Conan flag fix in CI
## [v0.2.5] - 2025-08-14
### Fixed
- **CI version bump**
- Updated git pages site
- Build system improvements
## [v0.2.4]
### Fixed
- **MCP Server Signal Handling**
- Server now responds properly to Ctrl+C (SIGINT) signals
- Replaced std::signal with sigaction to allow interrupting blocking I/O
- Added non-blocking stdin polling with 100ms timeout in StdioTransport
- Server checks external shutdown flag in main loop
- Handles EINTR errors and clears stdin error state properly
- Added clear startup messages and usage instructions to stderr
- **Dockerfile**
- Dockerfile should build correctly
- **Cross-Compilation Support**
- Added explicit Conan profiles for x86_64 and ARM64 architectures
- CI/CD workflows now properly handle cross-compilation with dual profiles
- Fixed zstd assembly symbol errors when cross-compiling on Apple Silicon
- Added zstd/*:build_programs=False option to avoid build issues
- Workflows detect native vs cross-compilation scenarios automatically
### Added
- **MCP Server Documentation**
- Comprehensive MCP usage guide at `docs/user_guide/mcp.md` (I personally use the CLI)
### Technical Details
- **Signal Handling**: Uses sigaction with sa_flags=0 to interrupt blocking system calls
- **Non-blocking I/O**: Implements poll() on Unix/macOS for stdin availability checking
- **Cross-Compilation**: Uses Conan's dual profile system (-pr:b for build, -pr:h for host)
## [v0.2.3] - 2025-08-14
### Fixed
- **CI version bump**
- README updates (removed install instructions with curl, download binary)
- Build system improvements for docker files and release
## [v0.2.2] - 2025-08-14
### Fixed
- **Docker Build C++20 Configuration**
- Added explicit C++20 standard setting in Conan profile
- Fixed "Current cppstd (gnu17) is lower than required C++ standard (20)" error
- Ensures Docker builds use correct C++ standard matching project requirements
- **Release Notes Formatting**
- Fixed Conan profile output contaminating GitHub release descriptions
- Redirected debug output to stderr to keep release notes clean
- Release pages now display properly formatted markdown
- **macOS Cross-Compilation**
- Fixed Boost build failures when cross-compiling x86_64 on ARM64 macOS
- Disabled Boost.Locale and Boost.Stacktrace.Backtrace components that fail in cross-compilation
- Enables successful builds on Apple Silicon machines with Rosetta 2
### Changed
- **Docker Build Process**
- Switched from CMake presets to direct CMake commands with Conan toolchain
- Added ninja-build to Docker dependencies for faster builds
- More robust build process that doesn't rely on dynamically generated presets
## [v0.2.1] - 2025-08-13
### Fixed
- **Build System Standardization**: All workflows now use Conan exclusively
- Fixed CMake export errors for spdlog and other dependencies
- Release workflow migrated from plain CMake to Conan-based builds
- Ensures consistent dependency management across CI and release
- Resolves "target requires target that is not in any export set" errors
- **Docker Build Issues**
- Fixed Conan 2.0 command syntax (`conan profile show` instead of `conan profile show default`)
- Fixed CMake preset issues by using direct CMake commands with Conan toolchain
- Added ninja-build to Docker dependencies for faster builds
- Improved version handling: uses git tags for releases, `dev-<sha>` for development builds
- Fixed undefined variable warnings in Dockerfile labels
- Added proper build argument handling for YAMS_VERSION and GITHUB_SHA
- **Release Page Formatting**
- Fixed Conan profile output contaminating release notes
- Redirected debug output to stderr to keep release notes clean
### Changed
- **MIME Type Detection Default Behavior**
- MIME types are now detected automatically during add operations
- `repair-mime` command remains available for fixing existing documents
- Detection uses FileTypeDetector with both signature and extension methods
- **Docker Versioning Strategy**
- Tagged releases use semantic version from git tag
- Development builds use `dev-<short-sha>` format
- Provides clear distinction between releases and development builds
### Technical Details
- **Testing Interface**: MCP server now exposes test methods via conditional compilation
- `#ifdef YAMS_TESTING` enables test-specific public methods
- Replaces hacky `#define private public` approach
- Maintains encapsulation while allowing proper unit testing
- **Build Workflows**: Unified Conan usage with proper profiles and caching
- Conan profile detection with C++20 enforcement
- Package caching for faster builds
- Consistent preset usage (`conan-release`) across all platforms
## [v0.2.0] - 2025-08-13
### Added
- **LLM Ergonomics Enhancements**
- Added `--paths-only` flag to search command for LLM-friendly output (one file path per line)
- Enhanced codebase indexing workflows for AI agent integration
- Improved documentation in PROMPT-eng.md with LLM-optimized YAMS patterns
- Support for using YAMS as "memory layer for low context" in AI workflows
- Magic number patterns for `#include`, `import`, `function`, `class`, shebang lines, etc.
- Automatic programming language detection during recursive directory operations
- **Grep Command**: Full-featured regex search within indexed file contents
- Standard grep options: `-A/--after`, `-B/--before`, `-C/--context` for context lines
- Pattern matching options: `-i` (case-insensitive), `-w` (whole word), `-v` (invert)
- Output options: `-n` (line numbers), `-H` (with filename), `-c` (count), `-l` (files with matches)
- Color highlighting support with `--color` option
- Supports searching all indexed files or specific paths
- **Knowledge Graph Integration in Get Command**
- Added `--graph` flag to display related documents
- Added `--depth` option (1-5) to control graph traversal depth
- Shows documents in same directory and with similar extensions
- Displays document relationships and metadata
- **Line-Level Search with Context**
- Enhanced search command with `-n/--line-numbers` flag
- Added context options: `-A/--after`, `-B/--before`, `-C/--context`
- Highlights matching lines with color
- Shows surrounding context lines for better understanding
- **C++17 Compatibility Mode** for broader system support
- New `YAMS_CXX17_MODE` CMake option for legacy compiler compatibility
- Support for GCC 9+, Clang 9+, older MSVC versions
- Automatic fallbacks: `boost::span` for `std::span`, `fmt` for `std::format`
- Compatible with Ubuntu 20.04 LTS, CentOS 8, older macOS versions
- Comprehensive compatibility documentation and build matrix
- Runtime feature detection with graceful degradation
- **Enhanced Build System Flexibility**
- Dual-mode compilation: full C++20 for modern systems, C++17 for legacy
- Automatic dependency management with Conan and FetchContent fallbacks
- Compiler-specific optimizations and warning configurations
- Performance-oriented feature selection based on available capabilities
- **MCP Server Feature Parity Enhancements** (~85% CLI-MCP parity achieved)
- **Enhanced search_documents tool** with LLM ergonomics optimizations
- Added `paths_only` parameter for LLM-friendly file path output (one per line)
- Added line context parameters: `line_numbers`, `after_context`, `before_context`, `context`
- Added `color` parameter for syntax highlighting control (always, never, auto)
- **New grep_documents tool** with full CLI grep parity
- Complete regex pattern matching across indexed document contents
- Context options: `-A/--after`, `-B/--before`, `-C/--context` for surrounding lines
- Pattern options: `ignore_case`, `word`, `invert` for flexible matching
- Output modes: `line_numbers`, `with_filename`, `count`, `files_with_matches`, `files_without_match`
- Color highlighting and `max_count` limit support
- **Knowledge graph integration** in retrieve_document tool
- Added `graph` parameter to include related documents in response
- Added `depth` parameter (1-5) for graph traversal control
- Added `include_content` parameter for full document content in graph responses
- Finds documents in same directory, similar extensions, and metadata relationships
- **New update_metadata tool** for document metadata management
- Update metadata by document `hash` or `name` with automatic resolution
- Support for multiple `key=value` metadata pairs in single operation
- Verbose output option for detailed update information
- **Enhanced list_documents tool** with comprehensive filtering and sorting
- File type filtering: `type`, `mime`, `extension`, `binary`, `text` parameters
- Time-based filtering: `created_after/before`, `modified_after/before`, `indexed_after/before`
- Recent documents filter: `recent` parameter for N most recent files
- Sorting control: `sort_by` (name, size, created, modified, indexed) and `sort_order` (asc, desc)
- **Enhanced get_stats tool** with file type breakdown analysis
- Added `file_types` parameter for detailed file type distribution
- Shows file type counts, sizes, top extensions per type, and top MIME types
- Provides comprehensive storage analytics for better content understanding
### Enhanced
- **MCP Tool Documentation** comprehensively updated with new schemas and examples
- Added complete JSON schemas for all enhanced tools with parameter descriptions
- Added practical usage examples for each tool capability
- Updated integration documentation for Claude Desktop configuration
- **YAMS-first workflow guidance**: default to indexing and searching code via YAMS pre-watch; avoid external grep/find/rg for repository queries.
- **CLI docs enhanced** with pre-watch indexing workflow and YAMS-only search/grep examples.
### Technical Details
- **File type classification system** with MIME type analysis using `getFileTypeFromMime()` and `isBinaryMimeType()` helper methods
- **Knowledge graph traversal** leverages document relationships through metadata repository queries
- **LLM ergonomics optimizations** reduce context usage while maintaining full functionality
- **Tool schema definitions** follow JSON-RPC standards for seamless MCP integration
### Fixed
- **Indexing Tests**: Updated for new API with proper factory function declarations
- **Namespace Issues**: Fixed forward declarations in document_indexer.h
- **CLI11 Conflicts**: Resolved `-h` flag conflict in grep command by using only `--no-filename`
- **Test Suite Stabilization**
- Fixed SEGV crash in vector_database_tests (DocumentChunkerTest bounds checking)
- Fixed AddressSanitizer container overflow in detection_tests
- Added thread safety to FixtureManager test infrastructure with proper mutex protection
- Added thread safety to FileTypeDetector for libmagic operations (not thread-safe by default)
- Fixed compilation errors in multiple test files (header includes, error codes, GMock dependencies)
- Fixed EXPECT_NO_THROW macro usage in detection tests
- **Recursive Add Pattern Parsing**
- Fixed CLI11 comma-separated pattern handling in `--include` and `--exclude` options
- Now properly splits patterns like `"*.cpp,*.h,*.md"` into individual patterns
- Added proper whitespace trimming and empty pattern filtering
- **CI/CD Pipeline Improvements**
- Fixed Conan options quoting for proper test builds (`"yams/*:build_tests=True"`)
- Added explicit `YAMS_BUILD_TESTS=ON` to CMake configuration
- Added individual test target builds before running ctest
- Implemented graceful test failure handling (CI continues, reports detailed results)
- Added ASAN relaxation options for CI environment compatibility
- Fixed YAML syntax error in release.yml (Python script indentation)
## [v0.1.3] - 2025-08-13
### Added
- **Multi-Channel Package Distribution System**
- Universal install script with platform detection (Linux/macOS, x86_64/ARM64)
- One-line installation: `curl -fsSL https://raw.githubusercontent.com/trvon/yams/main/install.sh | bash`
- Checksum verification and retry logic for secure downloads
- Custom installation directory support and shell completion setup
- Environment variable customization (YAMS_VERSION, YAMS_INSTALL_DIR, etc.)
- **Docker Container Support**
- Multi-stage Dockerfile with optimized Ubuntu-based runtime
- Multi-architecture builds (AMD64/ARM64) via GitHub Container Registry
- Automated publishing on tags and main branch pushes to `ghcr.io/trvon/yams`
- Non-root user configuration for security best practices
### Enhanced
- **GitHub Release Workflow with Performance Reporting**
- Comprehensive benchmark execution with JSON result collection
- Code coverage reports (HTML/XML) generated for Linux builds
- Performance metrics tables in release notes with timing and throughput data
- Coverage and benchmark files automatically uploaded as release assets
- Combined release notes with changelog and performance data
- **CI/CD Pipeline Improvements**
- Migrated all workflows to self-hosted runners (`self-hosted`, `Linux/macOS`, `X64/ARM64`)
- Fixed compatibility issues (mapfile command, artifact upload paths)
- Enhanced artifact collection (coverage reports, benchmark results, binaries)
- Streamlined build process removing problematic Conan profile modifications
### Notes
- All packaging improvements implemented but not yet released pending verification
- Release workflow enhanced to provide comprehensive performance and coverage data
- Multi-platform distribution ready for production deployment
## [0.1.2] - 2025-08-13
### Added
- **File Type and Time Filtering**: Enhanced list, get, and stats commands with comprehensive filtering
- File type filters: `--type`, `--mime`, `--extension`, `--binary`, `--text`
- Time filters: `--created-after/before`, `--modified-after/before`, `--indexed-after/before`
- Supports flexible time formats (ISO 8601, relative like "7d", natural like "yesterday")
- **Stats Command File Type Breakdown**: New `--file-types` flag shows detailed file type analysis
- File type distribution with counts and sizes
- Top file extensions per type
- Top MIME types in the system
- **Intelligent File Type Detection**: Uses magic_numbers.json as single source of truth
- Runtime detection of data files across multiple installation paths
- Graceful fallback to built-in patterns when JSON not found
### Changed
- **File Type Classification**: More accurate detection using magic numbers vs just extensions
- **Data File Installation**: magic_numbers.json now properly installed to system paths
## [0.1.1] - 2025-08-13
### Fixed
- Corrected Conan preset names (use `conan-release` instead of `build-conan-release`)
- Fixed C++20 standard requirement in Conan profiles
- Removed overly strict compiler warnings that broke dependency builds
- Fixed gcovr regex patterns for coverage reports
- Removed `-Wold-style-cast`, `-Wconversion`, `-Wsign-conversion`, and `-Woverloaded-virtual`
- Keeps essential warnings while allowing third-party code to compile cleanly
### Changed
- **Build Instructions**: Standardized on `conan-release` preset across all platforms
- Simplified build commands in README and documentation
- Consistent build directory structure (`build/conan-release`)
## [0.1.0] - 2025-08-12
### Added
- **List Command Enhancement**: Added `--recent N` flag to show N most recent documents
- Filters to the N most recent documents before applying other sorting
- Works with all existing sort options (name, size, date, hash)
- Useful for quickly viewing recently added content
- **PDF Text Extraction**: Full PDF text extraction support using PDFium library
- Extract text from all PDF pages with proper UTF-16 to UTF-8 conversion
- Extract PDF metadata (title, author, subject, keywords, creation date)
- Support for searching within PDFs with context lines
- Page-by-page extraction with configurable options
- Automatic section detection for academic papers
- **Metadata Update Command**: New `update` command for modifying document metadata
- Update metadata by document hash or name
- Support for multiple key-value pairs in single command
- Enables task tracking and status management workflows
- Works with both file and stdin documents
- **Task Tracking System**: Comprehensive benchmark and test enhancement tracking
- PBI documentation structure for systematic improvement
- Task status tracking via metadata updates
- Progress monitoring capabilities
- **KG Hybrid Scoring (default)**: Hybrid search integrates Keyword + Vector + Knowledge Graph
- Enabled by default in both CLI and MCP via a shared SearchEngineBuilder
- Fails open to metadata/keyword-only when KG is unavailable
### Fixed
- **Reference Counter Transaction IDs**: Fixed UNIQUE constraint violation in ref_transactions
- Removed manual transaction ID management
- Now uses SQLite AUTOINCREMENT for guaranteed unique IDs
- Prevents "UNIQUE constraint failed" errors when multiple ReferenceCounter instances exist
- **Duplicate Document Handling**: Fixed metadata constraint errors when re-adding existing documents
- Detects high deduplication ratio (≥99%) and updates existing metadata instead of inserting
- Properly handles both new and existing documents
- Updates indexed timestamp for existing documents
- **Name Resolution for Commands**: Fixed document lookup by name for stdin documents
- get, cat, and update commands now properly find stdin documents by name
- Uses search functionality as fallback when path-based search fails
- Supports both file-based and stdin documents uniformly
- Automatic platform detection (mac-arm64, mac-x64, linux-x64, linux-arm64, win-x64)
- FetchContent integration for non-Conan builds
- Conditional compilation with YAMS_HAS_PDF_SUPPORT flag
- Installs libpdfium.dylib into the install lib directory and sets its install_name to @rpath/libpdfium.dylib
- Patches installed executables to reference @rpath/libpdfium.dylib and adds rpath @loader_path/../lib
- Eliminates dyld errors like "Library not loaded: ./libpdfium.dylib"
- Created header file for UpdateCommand class
- Fixed compilation errors in update_command.cpp
- Resolved conflicts between Conan and FetchContent for Google Benchmark
- Fixed imgui.h include path for browse_command.cpp
- Fixed compilation issues with performance benchmarks
### Changed
- **Extraction Module**: Enhanced to support multiple file formats
- Modular extractor registration system
- Extensible architecture for future format support
- **Logging Verbosity**: Storage operations now use debug level instead of info
- "Stored file" messages only appear in verbose/debug mode
- Cleaner output for normal operations
### Known Issues
- **Performance Benchmarks**: Storage benchmarks cause segmentation fault after Rabin chunking tests
- SHA256 benchmarks work correctly (2.59 GB/s for large files)
- Rabin chunking benchmarks work correctly (178 MB/s)
- Storage fixture initialization causes crash - to be fixed in future update
## [0.0.6] - 2025-08-11
### Added
- TUI Browser Improvements
### Fixed
- Fixed unique_ptr copy errors in query parser benchmarks
- Resolved compression error handler warnings on Ubuntu 22.04
- Improved error handling and warning cleanup for better compiler compatibility
- Removed hardcoded widget dimensions that broke small terminal displays
- Fixed non-functional scrolling in document lists
- Improved loading state management and race condition handling
- Enhanced document preview formatting and metadata display
## [0.0.5] - 2025-08-11
### Added
- **Build System Enhancements**:
- Automatic std::format detection with fallback to fmt library for older compilers
- Improved ncurses detection for Linux builds with clear error messages
- BUILD-GCC.md documentation for building with GNU toolchain
- **Search Improvements**:
- Word-by-word processing for multi-word queries (e.g., "chain event ingestion" searches each word independently)
- Minimum-should-match scoring (50% of query words must match by default)
- Intelligent result aggregation with boost for documents matching all query words
- Edit distance-based scoring (closer matches score higher)
- Automatic fallback to fuzzy search when FTS5 fails
- **Hash search capability**: Search documents by SHA256 hash (full or partial, minimum 8 characters)
- **Verbosity control**: Concise output by default, detailed output with --verbose flag
- Auto-detection of hash format in queries (8-64 hexadecimal characters automatically trigger hash search)
- **MCP Server Enhancements**:
- Updated to use metadata repository path with all v0.0.5 search improvements
- Added fuzzy search support to MCP server tools with configurable similarity threshold
- Enhanced search_documents tool with fuzzy and similarity parameters
### Fixed
- Proper handling of hyphens in queries like "PBI-6", "task-4", "feature-123"
- Special characters (@, #, ?, :, /, \, [], {}, ()) no longer cause SQL errors
- Advanced FTS5 operators (AND, OR, NOT, NEAR) still available for power users
- **Fuzzy search matching**: Completely rewrote trigram similarity calculation
- **CI/CD Pipeline**:
- Added install step verification to ensure artifacts are created
- Added libncurses-dev to Ubuntu dependencies
- Enabled Ubuntu traditional (non-Conan) builds in CI matrix
### Changed
- **Search indexing strategy**: Enhanced to support both single and multi-word queries effectively
- Documents now indexed at word level in addition to full content
- Keywords extracted more comprehensively with 2-word phrases
- Improved tokenization with punctuation handling
- **Error handling**: FTS5 failures now gracefully fall back to fuzzy search instead of returning errors
## [0.0.4] - 2025-08-11
### Added
- **Directory-based workflows** with collections and snapshots for multi-folder ingestion
- `add --collection <name>`: Add documents to a named collection for organization
- `add --snapshot-id <id> --snapshot-label <label>`: Add documents to a snapshot for point-in-time grouping
- `add --recursive`: Recursively add files from directories
- `restore --collection <name>`: Restore all documents from a specific collection
- `restore --snapshot-id <id>`: Restore all documents from a specific snapshot
- `restore --layout <template>`: Flexible output patterns like `{collection}/{path}` for restore operations
- **MCP Server Tools** for directory operations with full CLI parity
- `add_directory`: Add directory contents with collection/snapshot support
- `restore_collection`: Restore documents from a collection to filesystem
- `restore_snapshot`: Restore documents from a snapshot to filesystem
- `list_collections`: List available collections
- `list_snapshots`: List available snapshots
- **CLI verbosity control**: All CLI commands now have concise output by default
- Use `--verbose` flag for detailed JSON metadata output
- Reduces context window usage while maintaining functionality
- **MCP Server enabled by default** in all builds for integrated AI tool support
### Changed
- **Database schema enhanced** with collections and snapshots metadata (migration v6)
- New indexes for efficient collection and snapshot queries
- Metadata tables support `collection`, `snapshot_id`, and `snapshot_label` fields
- **CLI output standardized** to be concise by default, verbose on request
- **Build system updated** to enable MCP server by default in Conan builds
### Fixed
- **Version consistency**: MCP server now uses same version system as CLI (was hardcoded "1.0.0")
- **ImTUI integration**: Resolved ncurses symbol versioning conflicts using ExternalProject_Add
- **FTS5 support**: Enabled SQLite full-text search in Conan configuration
- **Conan 2.0 compatibility**: Fixed all C++20 build issues with external dependencies
- **Test suite improvements**: Comprehensive fixes for CI/CD reliability
- Fixed GMock header compilation errors in MCP tests (missing `GTest::gmock` dependency)
- Fixed SlidingWindowChunker infinite loop caused by unsigned integer underflow
- Updated chunker test expectations to use realistic tolerances for word boundary preservation
- Fixed metadata repository tests API compatibility (ConnectionPool vs Database constructor)
- Resolved performance-dependent test failures in Rabin chunker (reduced expectations from 200MB/s to 100MB/s)
### Developer Notes
- Database migration system handles schema updates automatically
- All directory operations are scoped to prevent accidental mass operations
- MCP server integration provides seamless AI tool access to YAMS functionality
- Build system now supports both CLI and MCP server components by default
## [0.0.3] - 2025-08-11
### Added
- **MCP Tools**: New Model Context Protocol tools supporting v0.0.2 CLI enhancements
- `delete_by_name`: Delete documents by name, multiple names, or glob patterns with dry-run support
- `get_by_name`: Retrieve document content by name instead of hash
- `cat_document`: Display document content directly (similar to CLI cat command)
- `list_documents`: List stored documents with filtering by pattern and tags
- **TUI Browser migrated to ImTUI**: Complete rewrite from FTXUI to ImTUI for better compatibility
- Full-screen document viewer with hex mode toggle (Enter to open, x to toggle)
- External pager integration (o key) with proper terminal suspend/resume
- Preview pane scrolling when focused (Tab to switch columns, j/k to scroll)
- Extended command mode (:hex, :open, :refresh, :help, :q)
### Changed
- Browse command refactored to use modular TUI components and improved UX
### Fixed
- Safer preview of binary content and better CRLF handling
- **Build System**: Resolved multiple compilation issues preventing CI/CD success
- Fixed switch statement scope error in `posix_storage.cpp` by adding proper braces
- Added missing `#include <sys/resource.h>` for POSIX resource limits
- Added missing `#include <cmath>` in embedding tests for `std::isfinite` and `std::sqrt`
- Added missing `#include <algorithm>` for `std::all_of` in manifest manager
- Fixed designated initializer field ordering in `compressed_storage_engine.cpp`
- Fixed type conversion from `std::string_view` to `Hash` type
- Replaced `std::ranges::all_of` with `std::all_of` for broader compiler compatibility
### Developer Notes
- All compilation fixes tested locally with successful build completion
- Prepared for GitHub Actions CI/CD pipeline success
- Build now completes without errors on macOS (AppleClang 17.0.0)
## [0.0.2] - 2025-08-11
### Added
- **Name-based operations**: All major commands now support name-based access
- `delete --name <name>`: Delete document by name
- `delete --names <name1,name2>`: Delete multiple documents by names
- `delete --pattern <pattern>`: Delete documents matching glob pattern (e.g., `*.log`)
- `get --name <name>`: Retrieve document by name
- `cat` command: New command for displaying content directly to stdout
- `cat <hash>` or `cat --name <name>`: Output content for piping and viewing
- **Command aliases**: Unix-style command aliases for better ergonomics
- `rm` as alias for `delete`
- `ls` as alias for `list`
- **Delete command enhancements**:
- `--dry-run` flag: Preview what would be deleted without actually deleting
- `--verbose` flag: Show detailed deletion information
- Bulk deletion support with pattern matching
- Improved error handling for ambiguous names
- **Browse command improvements**:
- Command mode with `:` or `p` key (vi-like commands)
- Preview pane now shows actual content from metadata repository
- Binary content detection for preview
- Better search functionality with fuzzy/exact toggle
- **Documentation**:
- Added MCP tools documentation (`docs/api/mcp_tools.md`)
- Updated CLI documentation with new features
- Added this CHANGELOG.md for tracking changes
### Fixed
- **CI/CD**: Fixed compilation errors by adding missing includes in `compressor_interface.h`
- Added `#include <functional>`
- Added `#include <unordered_map>`
- **Browse command**: Fixed preview loading for documents with metadata content
### Changed
- **Get command**: Now supports both hash and name-based retrieval
- **Delete command**: Refactored to use CLI11 option groups for better argument handling
- **Browse command**: Enhanced with command mode and better content preview
### Developer Notes
- Integration tests created for delete command functionality
- Improved CLI command structure using option groups
- Better separation of concerns between viewing (`cat`) and downloading (`get`) operations
## [0.0.1] - 2025-08-11
### Added
- Initial release of YAMS
- Core content-addressable storage functionality
- MCP (Model Context Protocol) server support
- Basic CLI commands: init, add, get, delete, list, search
- Metadata repository with SQLite backend
- Compression support with multiple algorithms
- Deduplication at chunk level
- TUI browser interface
- Authentication and key management
- Configuration management
- Stats and monitoring capabilities
---
*Note: This project follows semantic versioning. Given the 0.x.y version, the API is still considered unstable and may change between minor versions.*
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