# Changelog Archive: v0.7.x Series


## [v0.7.7] - 11-07-2025 

### Added
- Hierarchical Embedding Architecture & Two-Stage Hybrid Search
  - Data model extensions for hierarchical embeddings
    - Added `EmbeddingLevel` enum (CHUNK, DOCUMENT) to distinguish embedding granularity
    - Extended `VectorRecord` with `level`, `source_chunk_ids`, `parent_document_hash`, `child_document_hashes` fields
    - Modified `embed_and_insert_document` to generate document-level embeddings (normalized mean of chunk vectors)
    - Document-level embeddings stored alongside chunk-level for two-stage search readiness
    - Added `twoStageVectorSearch` method that retrieves broader candidate set and applies hierarchical boosting
    - Configuration fields: `enable_two_stage`, `doc_stage_limit`, `chunk_stage_limit`, `hierarchy_boost`
    - Groups results by document and boosts scores based on document-level similarity
    - Wired into both parallel and sequential search paths for transparent operation
  - Profiling build support for performance analysis
    - New build type: `./setup.sh Profiling` enables instrumentation for Tracy, Valgrind, Perf
    - Builds to `build/profiling` directory with debug symbols + profiling hooks
    - Fuzzing build stub: `./setup.sh Fuzzing` reserved for future AFL++/libFuzzer integration
    - See `docs/developer/profiling.md` for comprehensive profiling guide
- **EmbeddingService Architecture**
  - **Problem**: PostIngestQueue workers were blocking on slow embedding generation, causing:
    - Documents not searchable until embeddings complete
    - Add commands hanging/timing out
    - Ingest pipeline stalled waiting for embedding models
  - **Solution**: Separated embedding generation into dedicated `EmbeddingService` that consumes from `InternalBus`
    - PostIngestQueue now 2-stage pipeline (Metadata + KnowledgeGraph) - embeddings removed
    - Documents searchable immediately after FTS5 indexing (~milliseconds)
    - Embeddings generated asynchronously in background by EmbeddingService workers
    - Better resource isolation: ingest and embedding workers independently tunable
    - No more blocking: add commands return immediately, documents queryable right away
- **ServiceManager & Daemon Lifecycle Improvements**
  - **Structured Concurrency**: Replaced manual backpressure logic with `std::counting_semaphore` for natural bounded concurrency
  - **SocketServer Improvements**: 
    - Converted async_accept to `as_tuple` pattern, eliminating exception overhead during shutdown
    - Connection future tracking for graceful shutdown with 2s timeout verification
  - **Modern Error Handling**: Consistent use of `boost::asio::as_tuple(use_awaitable)` for error codes instead of exceptions
  - **Future Tracking**: Replaced detached spawns with `use_future` for verifiable connection lifecycle management
- **Doctor Prune Command**: Intelligent cleanup of build artifacts, logs, cache, and temporary files
  - Support for 9 build systems (CMake, Ninja, Meson, Make, Gradle, Maven, NPM/Yarn, Cargo, Go)
  - Detection across 10+ programming languages (C/C++, Java, Python, JavaScript, Rust, Go, OCaml, Haskell, Erlang, etc.)
  - Hierarchical category system: build-artifacts, build-system, logs, cache, temp, coverage, IDE
  - **Extended package manager support**: Added 9 new categories for package dependencies and caches
    - IDE-specific: `ide-vscode`, `ide-intellij`, `ide-eclipse` for workspace caches
    - Dependencies: `package-node-modules` (npm/yarn/pnpm), `package-composer-vendor` (PHP), `package-cargo-target` (Rust)
    - Caches: `package-python-cache` (__pycache__/), `package-maven-repo`, `package-gradle-cache`, `package-go-cache`, `package-gem-cache`, `package-nuget-cache`
    - Composite groups: `package-deps`, `package-cache`, `packages` (all), `ide-all`
    - Path-based detection for directories: node_modules/, __pycache__/, .vscode/, target/, vendor/, etc.
  - Dry-run by default with `--apply` flag for execution
  - Usage: `yams doctor prune --category build-artifacts --older-than 30d --apply`
  - Usage: `yams doctor prune --category packages --apply` (clean all package artifacts)
- Started C++23 Compatibility support expansion
- Migrated vectordb to [https://github.com/trvon/sqlite-vec-cpp](https://github.com/trvon/sqlite-vec-cpp)
- **Tree-sitter Symbol Extraction Plugin** Enhanced multi-language symbol extraction with Solidity support
  - **Solidity Support**: Added complete Solidity language support with 4 query patterns (functions, constructors, modifiers, fallback/receive)
  - **Enhanced C++ Patterns**: 16 function patterns + 6 class patterns including templates, constructors, destructors, operator overloads, method declarations inside class bodies
  - **Multi-Language Improvements**: Enhanced patterns for Python (decorated functions), Rust (impl/trait methods), JavaScript/TypeScript (arrow functions, generators, async), Kotlin (property declarations) across all 15 supported languages
  - **Critical Bug Fix**: Fixed query execution early-return bug that caused pattern short-circuiting - now executes all patterns resulting in **2.2x recall improvement** (20.6% → 45.1%)
  - **Benchmark Infrastructure**: Catch2-based benchmark suite with quality metrics (Recall/Precision/F1), performance metrics (Throughput/Latency), and JSON output for CI integration
  - **GTest Suite**: 7 Solidity tests covering ERC20 tokens, inheritance, interfaces, events, and modifiers (372 lines, all passing)
  - Plugin auto-downloads tree-sitter grammars on first use (configurable via `plugins.symbol_extraction.auto_download_grammars`)
  - CLI commands: `yams config grammar list/download/path/auto-enable/auto-disable`
  - Supports tree-sitter v13-15 grammar versions
- **Entity Graph Service**: Background service for extracting and materializing code symbols into Knowledge Graph
  - Wired into IndexingPipeline and RepairCoordinator for automatic symbol extraction
  - Supports plugin-based language-specific symbol extraction
  - Foundation for symbol-aware search and code intelligence features
- **Database Schema v16**: Added `symbol_metadata` table for rich symbol information storage
  - Stores symbol definitions, references, and metadata from code analysis plugins
  - Indexed by document hash and symbol name for efficient lookups
  - Integrated with Knowledge Graph for entity relationship tracking
  - Migration includes tests for both schema changes and symbol metadata storage
- **Symbol-Aware Search Infrastructure**: Enhanced search with symbol/entity detection and enrichment
  - `SymbolEnricher` class extracts rich metadata from Knowledge Graph (definitions, references, call graphs)
  - Symbol context includes type, scope, caller/callee counts, and related symbols
  - **Hybrid Search Symbol Integration**: Symbol metadata now actively boosts search ranking
    - Added `symbol_weight` configuration field (default: 0.15 = 15% multiplicative boost)
    - `HybridSearchEngine::setSymbolEnricher()` method wires SymbolEnricher into search pipeline
    - Symbol matches receive score boost when `isSymbolQuery && symbolScore > 0.3`

### Fixed
- **Grep Command Duplicate Output**: Fixed `yams grep` printing results twice when stderr is redirected
- **Migration System Crash (macOS)**: Fixed SIGSEGV crash in `MigrationManager::recordMigration()` during daemon startup
  - **Root Cause**: `ServiceManager::co_migrateDatabase()` called `mm.initialize()` but ignored its return value. If initialization failed to create the `migration_history` table, migrations would continue and crash when attempting to INSERT into the non-existent table.
  - **Fix**: Added error checking for `mm.initialize()` with early return and proper error logging in `ServiceManager.cpp`
- **Embedding System Architecture Simplification**: Simplified FSM readiness logic to check provider availability directly instead of waiting for model load events
  - IModelProvider checks `isAvailable()` immediately after plugin adoption
  - Eliminates unnecessary ModelLoading state transition
  - Fixes "Embedding Ready: Waiting" status showing incorrectly when embeddings were actually available
  - Model dimension retrieved via `getEmbeddingDim()` at adoption time
- **Database Schema Recovery**: Manual creation of missing `kg_doc_entities` table from migration 7
  - Table includes 8 columns with foreign keys to documents and kg_nodes
  - Created indexes: `idx_kg_doc_entities_document`, `idx_kg_doc_entities_node`
  - Fixes search query errors: "no such table: kg_doc_entities"
- **Worker Thread Premature Exit**: Fixed io_context workers exiting immediately on startup by adding `executor_work_guard` to keep the context alive until explicit shutdown.
- **SocketServer Backpressure**: Manual backpressure polling with `std::counting_semaphore`, eliminating 5-20ms delay loops and providing natural bounded concurrency.
- **Embedding Consumer Deadlock**: Fixed race condition causing embedding job consumer to stall
  - Added defensive retry mechanism with exponential backoff for queue state recovery
  - Impact: Embedding background processing now reliable under high load
- **FSM Cleanup & Degradation Tracking**: Standardized FSM usage across ServiceManager
  - Added `DaemonLifecycleFsm` reference to ServiceManager for centralized subsystem degradation tracking
- **ServiceManager FSM Architecture**: Centralized state management and eliminated duplication
  - Added `DaemonLifecycleFsm& lifecycleFsm_` reference to ServiceManager for daemon-level degradation tracking
  - Removed scattered manual FSM state checks in favor of FSM query methods (`isReady()`, `isLoadingOrReady()`)
- **Text Extraction for Source Code**: Fixed critical issue where JavaScript/TypeScript/Solidity/config files failed FTS5 extraction
    - `src/extraction/extraction_util.cpp`: Replaced hardcoded `is_text_like()` with `FileTypeDetector::isTextMimeType()` which uses comprehensive `magic_numbers.hpp` database; added extension normalization (handles both `.js` and `js` formats)
    - `src/extraction/plain_text_extractor.cpp`: 
      - Removed hardcoded 50+ extension list, delegating to `FileTypeDetector` for dynamic detection
      - Enhanced `isBinaryFile()` with UTF-8 BOM support and reduced false positives
      - Added `isParseableText()` with proper UTF-8 validation (validates multi-byte sequences, continuation bytes)
      - Baseline registration now includes common config/markup extensions (`.toml`, `.ini`, `.yml`, `.md`, `.rst`)
    - `src/app/services/search_service.cpp`: Updated lightweight indexing to use `FileTypeDetector::isTextMimeType()`

### Changed
- **Embedding Provider Lifecycle**: Transitioned from event-driven model loading to direct availability checking
  - Provider adoption now immediately dispatches `ModelLoadedEvent` if `isAvailable()` returns true
  - Simplified from 4-state FSM (Unavailable → ProviderAdopted → ModelLoading → ModelReady) to immediate ready transition
  - Aligns FSM with IModelProvider on-demand model loading architecture

### Removed
- **Fuzzy Index Memory Optimization**: Enhanced BK-tree index building with intelligent document prioritization
  - Uses metadata and Knowledge Graph to rank documents by relevance (tagged > KG-connected > recent > code files)
  - Limits index to 50,000 documents by default (configurable via `YAMS_FUZZY_INDEX_LIMIT` environment variable)
  - Graceful degradation with `std::bad_alloc` handling prevents daemon crashes on large repositories
  - **Known Limitation**: Fuzzy search on very large repositories (>100k documents) may experience memory pressure. Consider using metadata/KG filters or grep with exact patterns for better performance
- **ONNX Plugin Model Path Resolution**: Enhanced model path search to support XDG Base Directory specification
- **Platform-Aware Plugin Installation**: Build system now auto-detects Homebrew prefix on macOS
  - `/opt/homebrew` on Apple Silicon, `/usr/local` on Intel Macs and Linux
  - System plugin directory automatically trusted by daemon at runtime
  - Override via `YAMS_INSTALL_PREFIX` environment variable
- Model loading timeouts hardened: adapter and ONNX plugin now use std::async with bounded wait; removed detached threads causing UAF/segfaults (AsioConnectionPool guarded)
- Vector DB dim resolution no longer hardcodes 384; resolves from DB/config/env/provider preferred model, else warns and defers embeddings
- ONNX plugin: removed implicit 384 defaults, derives embeddingDim dynamically from model/config; added env override YAMS_ONNX_PRECREATE_RESOURCES
- Improved load diagnostics: detailed logs for ABI table pointers, phases, and timeout causes
- **Search Service Path Heuristic**: Tightened path-first detection to only trigger for single-token or quoted path-like queries (slashes, wildcards, or extensions). Multi-word queries now proceed to hybrid/metadata search, restoring results for phrases such as `"docs/delivery backlog prd tasks PBI"` while preserving fast path lookups for actual paths.

- Daemon stop reliability: `yams daemon stop` now only reports success after the process actually exits and will fall back to PID-based termination (and orphan cleanup) when the socket path is unresponsive.
- Prompt termination on signals: the daemon now handles SIGTERM/SIGINT to exit promptly when graceful shutdown isn't possible, addressing lingering yams-daemon processes after stop.
- **Hybrid Search Simplification**: Removed complexity and environment variable overrides
  - Removed 6 environment variables: `YAMS_DISABLE_KEYWORD`, `YAMS_DISABLE_ONNX`, `YAMS_DISABLE_KG`, `YAMS_ADAPTIVE_TUNING`, `YAMS_FUSION_WEIGHTS`, `YAMS_OVERRELIANCE_PENALTY`
  - Kept `YAMS_DISABLE_VECTOR` for CI compatibility
  - Removed adaptive weight tuning logic (~30 LOC)
  - Removed over-reliance penalty mechanism
  - Keyword search now always executes (controlled by `config.keyword_weight`)
  - Fixed fusion weights for `LEARNED_FUSION` strategy: `{-2.0f, 3.0f, 2.0f, 1.5f, 1.0f}`

### Removed
- Removed WASM, and legacy plugin system from codebase and ServiceManager

## [v0.7.6] - 10-13-2025
### Added
- **CLI Pattern Ergonomics**: Added `--pattern/-p` flag to `list` command as an alias for `--name`, improving consistency with other commands. The flag supports glob wildcards (`*`, `?`, `**`) and auto-normalizes relative paths to absolute when no wildcards are present. (`src/cli/commands/list_command.cpp`)
- **Grep Literal Text Hints**: Added smart error detection and helpful hints when grep patterns contain regex special characters. When a pattern fails regex compilation or returns no results, grep now suggests using the `-F` flag with the exact command to run. Added `-Q` as a short alias for `-F/--fixed-strings/--literal-text` to match git grep convention. (`src/cli/commands/grep_command.cpp`)
- **Search Literal Text Aliases**: Added `-F/-Q/--fixed-strings` aliases to `search` command for consistency with `grep`. These short flags make it easier to search for literal text containing special characters like `()[]{}.*+?`. Updated help text with concrete examples. (`src/cli/commands/search_command.cpp`)
- Grep: enabling `[search.path_tree]` now lets explicit path filters reuse the metadata-backed
  path-tree engine, and tag-only invocations default the pattern to `.*`, removing the need for
  placeholder expressions. citesrc/app/services/grep_service.cpp:240src/cli/commands/grep_command.cpp:305
- **Tree-based List with Filters**: Extended tree-based path queries to support tag, MIME type, and extension filtering. The `list` command now uses the tree index even when filters are applied, improving performance for pattern+filter queries (e.g., `yams list --name "docs/**" --tags "test"`).
- **Benchmark: Tree List Filters**: New benchmark suite (`tree_list_filter_bench`) measures query performance with various filter combinations. Results show 100-160μs query times with up to 10k queries/sec throughput. Filter queries often outperform path-only queries due to reduced result set sizes.
- **Grep SQL-Level Pattern Filtering**: Added `queryDocumentsByGlobPatterns()` function that converts glob patterns (e.g., `tests/**/*.cpp`) to SQL LIKE patterns and queries the database directly, eliminating the need to load all documents into memory before filtering. Grep performance with `--include` patterns improved dramatically on large repositories.
- **Search Multi-Pattern Support**: Added `pathPatterns` vector field to `SearchRequest` IPC protocol (field 34) enabling server-side filtering of multiple include patterns. Search command now sends all patterns to daemon instead of filtering results client-side, eliminating timeouts and OOM errors in sandboxed environments.
- **MCP Search Multi-Pattern Support**: Added `include_patterns` array parameter to MCP search tool, enabling clients to specify multiple path patterns with OR logic. The MCP server now populates `pathPatterns` in daemon requests, matching CLI behavior. (`include/yams/mcp/tool_registry.h`, `src/mcp/mcp_server.cpp`)

### Changed
- MCP stdio transport: stdout buffering now adapts to interactive vs non-interactive streams,
  stderr is forced unbuffered, and JSON-RPC batch arrays over stdio are parsed in-line to match
  the Model Context Protocol 2025-03-26 transport requirements. Additional unit coverage exercises
  batch handling and error budgets for framed headers.
- **MCP Server**: `cat` and `get` tools now resolve relative paths using `weakly_canonical`, improving document lookup for non-absolute paths.
- **Path Canonicalization**: Document paths are now canonicalized using `weakly_canonical()` at ingestion time to ensure consistent path matching across symlinked directories (e.g., `/var` → `/private/var` on macOS). This fixes pattern-based queries that previously failed due to path mismatch between indexed and query paths. (`src/metadata/path_utils.cpp`)
- **Integration Test Stability**: Improved `TreeBasedListE2E` test reliability by replacing fixed sleep with polling-based wait for document indexing completion. Test pass rate improved from ~60% to 100%.
- **Grep Performance**: Grep service now uses SQL-level pattern filtering when `--include` patterns are provided, fetching only matching documents from the database instead of loading all documents and filtering in memory. Converts glob patterns to SQL LIKE patterns (e.g., `*.cpp` → `%.cpp`, `tests/**/*.h` → `tests/%.h`). This eliminates hangs on large repositories (10K+ documents).
- **Search Service**: Updated to handle multiple path patterns via `pathPatterns` vector field, iterating through all patterns with OR logic for server-side filtering. Removed client-side filtering that previously caused timeouts with multiple `--include` patterns.
- **Build System**: Fixed VS Code task definitions with correct Conan 2.x output paths. Meson native file paths updated from `builddir/conan_meson_native.ini` to `builddir/build-debug/conan/conan_meson_native.ini` and `build/release/build-release/conan/conan_meson_native.ini` to match actual Conan 2 directory structure. (`.vscode/tasks.json`)

### Fixed
- **MCP Search/Grep Hang**: Fixed MCP server's `search` and `grep` tools hanging indefinitely by ensuring all async components use the same io_context. The root cause was a multi-layered async execution mismatch: (1) The DaemonClient's config didn't specify an executor, causing it to create its own internal io_context. (2) `callTool()` was spawning work on GlobalIOContext and blocking a worker thread waiting for results. (3) The two separate io_contexts couldn't communicate, causing deadlock. Fixed by: (a) Configuring daemon_client to use GlobalIOContext executor in MCPServer constructor. (b) Removing the nested local io_context from `callTool()` - now correctly spawns on GlobalIOContext (which has background worker threads) and waits for results. (c) Removing nested io_context from `handleSearchDocuments()` to use `co_await` directly. (`src/mcp/mcp_server.cpp:403,2029-2039,2225-2226`)
- **Document Service**: Improved `resolveNameToHash` to correctly handle filename-only lookups by searching for paths ending with the given name, ensuring that commands like `cat` with a simple filename succeed.
- **Tree Query Pattern Matching**: Fixed wildcard pattern parsing to correctly handle recursive patterns (`/**`) by stripping all trailing wildcards iteratively instead of checking for a single wildcard character. (`src/app/services/document_service.cpp`)
- **Grep Hang**: Fixed grep command hanging indefinitely when using `--include` patterns on large repositories. The service was fetching all documents before filtering; now uses SQL-level pattern matching to fetch only relevant documents.
- **Search Timeout**: Fixed search command timeouts/OOM when using multiple `--include` patterns. Previously only the first pattern was sent to daemon with remaining patterns filtered client-side after retrieving ALL results. Now all patterns are sent to daemon for server-side filtering.
- **Search Pattern Matching**: Fixed glob pattern normalization to correctly match filename patterns like `*.md` and `*.cpp` anywhere in the path tree. Patterns starting with a single `*` (e.g., `*.ext`) are now automatically prefixed with `**/` to match paths at any depth. This ensures patterns like

## [v0.7.4] - 2025-10-010

### Changed
- **MetadataRepository**: Added atomic counters (`cachedDocumentCount_`, `cachedIndexedCount_`, `cachedExtractedCount_`) updated on every insert/delete/update operation. Eliminated 3 `COUNT(*)` queries from hot path (220-400ms → <1μs)
- **VectorDatabase**: Added `cachedVectorCount_` atomic counter updated on insert/delete operations. Eliminated `COUNT(*)` query from `getVectorCount()` 
- **ServiceManager Concurrency**: Converted `searchEngineMutex_` from `std::mutex` to `std::shared_mutex` enabling N concurrent readers with single exclusive writer. Allows parallel status requests without serialization bottleneck
- **Status Request Optimization**: Removed blocking VectorDatabase initialization from hot path. Status handler now reports readiness accurately without attempting to "fix" uninitialized state, eliminating 1-5s blocking operations
- **Performance**: Sequential request throughput improved to ~1960 req/s with sub-millisecond latency (avg: 0.02ms, max: 1ms). First connection latency: 2ms. Daemon readiness validation added to prevent test methodology races with initialization
- **Document Retrieval Optimization**: Replaced O(n) full table scans with O(log n) indexed lookups in `cat`/`get` operations. Changed from `queryDocumentsByPattern('%')` → `getDocumentByHash(hash)` eliminating 120K+ document scans per retrieval (lines 850, 934 in document_service.cpp)
- **Name Resolution Fix**: Fixed pattern generation for basename-only queries. Now generates `'%/basename'` pattern FIRST to use `containsFragment` query instead of failing `exactPath` (path_hash) match. `yams get --name` and `yams cat <name>` now work correctly
- **Grep FTS-First**: Optimized grep to START with FTS5 index search for literal patterns before falling back to full document scan. Regex patterns still use full scan. Significantly improves grep performance on large repositories
- **ONNX Plugin**: Upgraded the ONNX plugin to conform to the modern `model_provider_v1` (v1.2) interface specification.
- Enhanced `ui_helpers.hpp` with 30+ new utilities: value formatters (`format_bytes`, `format_number`, `format_duration`, `format_percentage`), status indicators (`status_ok`, `status_warning`, `status_error`), table rendering (`Table`, `render_table`), progress bars, text utilities (word wrap, centering, indentation)
- Improved `yams status` with color-coded severity indicators, human-readable formatting, and sectioned layout
- Enhanced `yams daemon status` with humanized counter names (CAS, IPC, EMA, DB acronyms preserved), smart byte/number formatting
- Added `yams daemon status -d` detailed view with storage overhead breakdown showing disk usage by component (CAS blocks, ref counter DB, metadata DB, vector DB, vector index) with overhead percentage relative to content

### Deprecated
- **MCP `get_by_name` tool**: Use `get` tool with `name` parameter instead. The `get` tool now smartly handles both hash and name lookups with optimized pattern matching

- **Streaming Protocol Bug**: Fixed critical bug where `GetResponse`/`CatResponse` sent header-only frame (empty content) followed by data frame, causing CLI to process first frame and fail. Added `force_unary_response` check in request_handler.cpp to disable streaming for these response types, forcing single complete frame transmission
- **Protobuf Schema**: Added missing `bool has_content = 6` field to `GetResponse` message in ipc_envelope.proto. Updated serialization to explicitly set/read flag instead of recalculating, preventing desync between daemon and CLI
- **Daemon**: Fixed a regression in the plugin loader that prevented legacy model provider plugins (like the ONNX provider) from being correctly detected and adopted. The loader now includes a fallback to detect and register providers using the legacy `getProviderName`/`createProvider` symbols, restoring embedding generation functionality.
- **Grep Service**: Fixed critical bug where `--paths-only` mode returned all candidate documents without checking pattern matches, causing incorrect "(no results)" responses. Removed premature fast-exit optimization; grep now properly runs pattern matching and returns only files that match. (Issue: 135K docs indexed but grep returned empty, audit revealed fast-exit bypassed validation)
- **Grep CLI**: Fixed session pattern handling bug where session include patterns were incorrectly used as document selectors instead of result filters. Session patterns now properly merged into `includePatterns` for filtering, not `paths` for selection. This prevented grep from finding any results when a session was active.

## [v0.7.3] - 2025-10-08

### Added
- Bench: minimal daemon warm-start latency check moved to an opt-in bench target and suite.
  - New standalone binary `tests/yams_bench_daemon_warm` executes a bounded start/sleep/stop
    cycle with vectors disabled and tight init timeouts; asserts <5s end-to-end.
  - Meson test registered as `bench_daemon_warm_latency` in the `yams:bench` suite.
  - Disabled by default in CI; enable by setting `RUN_DAEMON_WARM_BENCH=true` (workflow env)
    and `YAMS_ENABLE_DAEMON_BENCH=1` (step env) to run only this bench.
- Tree-Diff Metadata & Retrieval Modernization🎉
  - **Tree-based snapshot comparison**: Implemented Merkle tree-based diff algorithm for efficient snapshot comparison with O(log n) subtree hash optimization for unchanged directories.
  - **Rename detection**: Hash-based rename/move detection with ≥99% accuracy, enabled by default in `yams diff` command.
  - **Knowledge Graph integration**: Path and blob nodes with version edges and rename tracking via `fetchPathHistory()` API.
  - **Enhanced graph command**: `yams graph` now queries KG store for same-content relationships and rename chains.
  - **Tree diff as default**: `yams diff` uses tree-based comparison by default; `--flat-diff` flag available for legacy behavior.
  - **RPC/IPC exposure**: Added `ListTreeDiff` method to daemon protocol (protobuf + binary serialization).

### Changed
- **Daemon Async Architecture**: Unified on modern Boost.Asio 1.82+ patterns with C++20 coroutines (`asio::awaitable`)
  - Single io_context with work guard for all async operations
  - Strands for logical separation (init, plugin, model domains)
  - RAII cleanup guards for automatic resource management
  - Error codes via `as_tuple` instead of exceptions for hot paths
  - Semaphore-based bounded concurrency instead of manual atomic flags
- **Compression-first retrieval** DocumentService, CLI, and daemon IPC now default to
  returning compressed payloads with full metadata (algorithm, CRC32s, sizes)
- **Path query pipeline**: Replaced the legacy `findDocumentsByPath` helper with the normalized `queryDocuments` API and the shared `queryDocumentsByPattern` utility. All services (daemon, CLI, MCP, mobile bindings, repair tooling, vector ingestion) now issue structured queries that leverage the `path_prefix`, `reverse_path`, and `path_hash` indexes plus FTS5 for suffix matches, eliminating full-table LIKE scans.
- **Schema migration**: Migration v13 (`Add path indexing schema`) continues to govern the derived columns/indices; applying this release replays the up hook in place (normalizing existing rows and rebuilding the FTS table), so existing deployments automatically benefit from the optimized lookups after the usual migration step.
- **CLI Retrieval (get/cat)**: partial-hash resolution now routes through `RetrievalService`
  using the daemon’s streaming search and the metadata-layer hash-prefix index.
  - `yams get` and `yams cat` accept 6–64 hex prefixes; ambiguity can be resolved via
    `--latest/--oldest`. No more local metadata table scans; latency improves especially on
    large catalogs.
  - Internals: `RetrievalService::resolveHashPrefix` consumes `SearchService` hash results and applies newest/oldest selection hints; `GetCommand` validates and normalizes hash input before issuing a daemon `Get`.

### Fixed
- **Daemon IPC:** Fixed a regression in the `grep` IPC protocol where `GrepRequest` and `GrepResponse` messages were not fully serialized, causing data loss. The protocol definitions and serializers have been updated to correctly handle all fields, including `show_diff` in requests and detailed statistics in responses.
- **Indexing**: Fixed an issue where updated files were not being re-indexed. The change detection logic now correctly considers file modification time and size, in addition to content hash, to reliably identify changes.
- **Indexing**: Corrected the document update process to prevent duplicate records for the same file path when a file is updated. The indexer now properly distinguishes between new documents and updates to existing ones.
- **Daemon IPC**: Fixed an issue where `search` and `grep` commands could time out without producing output by improving the efficiency of the daemon's streaming response mechanism.
- **Daemon IPC**: Optimized non-multiplexed communication paths to prevent performance issues and potential timeouts with large responses from commands like `get` and `cat`.

## [v0.7.2] - 2025-10-03

### Added
- Automatic directory snapshot generation with ISO 8601 timestamp IDs and git metadata detection (commit, branch, remote). Every `yams add <directory>` now creates a timestamped snapshot stored in the `tree_snapshots` table.
- Snapshot Listing: New `yams list --snapshots` command displays all available snapshots with table and JSON output formats, showing snapshot IDs, directory paths, labels, git commits, and file counts.
-  Implemented `yams diff <snapshotA> <snapshotB>` command with tree, flat, and JSON output formats for comparing directory snapshots.
- TreeDiffer automatically detects renamed/moved files via SHA-256 hash equivalence matching, enabled by default.

### Changed
- **Snapshot Labels**: `yams add` now accepts optional `--label` flag for human-readable snapshot names.
- **Indexing Service**: Enhanced to persist snapshot metadata (snapshot_id, directory_path, git metadata, file count) to database after directory ingestion.
- **Metadata Repository**: Added `upsertTreeSnapshot()`, `listTreeSnapshots()`, and tree diff persistence methods for snapshot and change history management.
- Search: Parallelized keyword search scoring loop to significantly improve performance on multi-core systems.
- Search: Search thread pools are now configured by the central `TuningManager` to adapt to system load and tuning profiles.
- Search: Implemented structural scoring to boost relevance of results that are co-located in the same directory.
- Search: Parallelized keyword search scoring loop to significantly improve performance on multi-core systems.
- Search: Search thread pools are now configured by the central `TuningManager` to adapt to system load and tuning profiles.
- Search: Implemented structural scoring to boost relevance of results that are co-located in the same directory.
- Added FTS5 readiness fast-path check in `getByNameSmart()` to prevent 3-second blocking timeouts when search indexes are updating. 
- Added `post_ingest_queue_depth` field to status response, enabling clients to check if FTS5 indexes are ready before attempting expensive search operations.
- TUI browse command now resolves listings and fuzzy search through the shared AppContext service bundle (`TUIServices` + `IDocumentService`/`ISearchService`), with graceful fallback to metadata/content-store paths when the daemon is degraded.
- CLI Browse: Shift+R reindex dialog now performs a full extraction + index refresh through `TUIServices::reindexDocument`, providing inline success/error feedback instead of the previous placeholder flow.

### Fixed
- Daemon IPC: SocketServer now shares a live writer-budget reference with every connection and the tuning manager pushes updates through it. Multiplexed streams adjust bandwidth limits immediately when profiles or runtime heuristics change.
- Search: Corrected an issue where `yams search --include` was not being applied for hybrid searches. The include pattern is now passed to the daemon and correctly filters results.
- Fixed protobuf UTF-8 validation errors when grepping binary files or non-UTF-8 text. Changed `GrepMatch.line`, `context_before`, and `context_after` fields from `string` to `bytes` type in protobuf definition. This allows grep to handle arbitrary byte sequences including binary content, Latin-1, Windows-1252, and other legacy encodings without validation failures. (PBI-001, task 001-33)
- Daemon IPC: replaced the `io_context.run_for` polling loop with dedicated `run_one` workers so async accept completions are no longer starved during streaming requests. Added optional diagnostic thread (`YAMS_SOCKET_RUN_DIAG`) for debugging.
- CLI Browse: refuse to launch the FTXUI browser when the terminal is non-interactive, lacks TERM capabilities, or is smaller than 60x18; emit a clear resize guidance message instead of hanging or crashing.
- CLI Search: release pooled daemon clients before process teardown to prevent the `std::system_error: mutex lock failed` abort when `yams search` exits after hitting the daemon path.

## [v0.7.1] - 2025-09-29

### Changed
- GrepService: expanded candidate discovery to preselect from `req.paths` using SQL LIKE prefix scans, aligning service behavior with CLI expectations for directory patterns.
- RepairCoordinator refocus: on live `DocumentAdded` events, skip queuing when the post‑ingest
- Post‑ingest pipeline: improvements
- ServiceManager enqueue path: simplified `enqueuePostIngest` to a direct blocking enqueue. This improves predictability and throughput under high load.
- CLI Download UX: `yams download` now clearly displays the ingested content hash

### Fixed
- GrepService streaming: flushes the final partial line when scanning cold CAS streams so single-line files are matched reliably (e.g., `hello.txt`).
- Reduced GrepService log verbosity to `debug` for internal counters and match traces.
- Fixed IPC protocol regression where grep and list commands failed to properly communicate with the daemon after migration, causing incomplete results or timeouts in multi-service environments.
  - This issue impacted other tools result output 
- Guarded compression monitor global statistics with a dedicated mutex to stop concurrent tracker
  updates from crashing `unit_shard5` (validated via `meson test -C build/debug unit_shard5
  --print-errorlogs`).
- Repaired the `document_service` metadata pipeline regression so fixture-driven search tests no
  longer observe missing extracted content.
- MCP stdio transport: replaced unused static output mutex with an instance mutex to satisfy
  ODR/build on certain platforms.

## [v0.7.0] - 2025-09-25

### Highlights
- These changes reduce CPU spikes observed in profiles for large greps and remove
  blocking storage scans from interactive status paths. Post-ingest work is intentionally
  bounded; processing may take longer, but overall system responsiveness improves.
- Stability: resolved connection timeouts under multi-agent load by removing the hard
  100-connection cap and deriving a dynamic accept limit. Defaults honor
  `YAMS_MAX_ACTIVE_CONN` or compute a safe cap from CPU cores and IO concurrency.
- Throughput: added tuning profiles (efficient | balanced | aggressive). Profiles modulate
  pool growth, IO thresholds, and post-ingest workers. Default is `balanced`.
- Indexing UX: Add/ingest returns fast; post‑ingest queue handles FTS/embeddings/KG in the
  background. Path‑series versioning (Phase 1) is on by default behind an env flag.

### Added
- Tuning profiles selectable via config or env:
  - Config: `yams config set tuning.profile <efficient|balanced|aggressive>`
  - Env: `YAMS_TUNING_PROFILE=<profile>`
- Config defaults now include `[tuning] profile = "balanced"`.
- Docs: `docs/admin/tuning_profiles.md` covering profiles, envs, and observability.
- Versioning (Phase 1): path‑series lineage with `VersionOf` edges and metadata flags
  `version`, `is_latest`, `series_key`. Duplicate (same hash) re‑ingest does not create a new
  version; alternate locations and timestamps are updated.

- CLI Search: grouped multi‑version presentation (default on) with new controls.
  - Groups results by canonical path when multiple versions of the same file are returned.
  - New flags:
    - `--no-group-versions` — disable grouping and show the flat list.
    - `--versions <latest|all>` — choose best only (default: latest) or list versions per path.
    - `--versions-topk <N>` — cap versions shown per path when `--versions=all` (default: 3).
    - `--versions-sort <score|path|title>` — sort versions within a group (default: score).
    - `--no-tools` — hide per‑version tool hints.
    - `--json-grouped` — emit grouped JSON; plain `--json` remains flat and backward compatible.
  - Tool hints shown per version (when grouped):
    `yams get --hash <hash> | yams cat --hash <hash> | yams restore --hash <hash>`;
    if a local file path is resolved, a `yams diff --hash <hash> <local-path>` hint is added.
  - Environment toggles: `YAMS_NO_GROUP_VERSIONS=1` and `YAMS_NO_GROUP_TOOLS=1` to flip defaults.
  - Note: This is a presentation‑layer change; service/daemon APIs are unchanged.

### Changed
- **Build System**
  - The primary build system has been migrated from CMake to Meson. All build, test, and packaging scripts have been updated to use the new Meson-based workflow.
- Status/Stats (CLI): use daemon metrics by default and never trigger local storage scans.
  - `yams status` and `yams stats -v` now render from the same non-detailed daemon snapshot;
    removed the "scanning storage..." spinner and filesystem walks.
  - Verbose output formats the JSON fields instead of performing extra scans.
- Tools/Stats (yams-tools): `tools/yams-tools/src/commands/stats_command.cpp` refactored to
  prefer daemon-first metrics with a legacy local fallback only if daemon is unavailable.
- MCP add_directory: switched to daemon-first ingestion with a brief readiness wait to avoid
  "Content store not available" races. Removes local store preflight; maps NotInitialized to a
  clear, retryable message from the daemon.
- MCP search: path normalization + optional diff parity with CLI.
  - New request field `include_diff` adds a structured `diff` block to results when the
    `path_pattern` points to a local file; mirrors `yams search` diff behavior.
  - MCPSearch DTOs extended to round-trip `include_diff`, `diff`, and `local_input_file`.
- Daemon accept scaling: removed fixed cap; now dynamically computes `maxConnections` from
  `recommendedThreads * ioConnPerThread * 4` (min 256) unless `YAMS_MAX_ACTIVE_CONN` is set.
- Backpressure: increased default read pause to 10ms to smooth heavy load.
- Post‑ingest: preserves bounded capacity; de‑dupes inflight, indexes FTS, updates fuzzy index,
  and emits KG nodes/edges best‑effort.
- Status/Stats: JSON correctness improvements; omit misleading savings when physical size
  unknown; surface post‑ingest bus usage and document counters.
- CLI Search: grouping of multiple versions per path is enabled by default; paths‑only output
  and flat JSON remain unchanged unless `--json-grouped` is specified.

### Fixed
- Regression in metadata extraction and storage used in search and grep tools
  The async post-ingest pipeline never persisted extracted text into the metadata store. As a result, document_content stayed empty, so search, repairs, and semantic pipelines saw “Document content not found” despite vector insert logs.
- Many tuning optimizations for daemon usage
- Grep pipeline: staged KG → metadata → content with caps and budget.
  - Prefers "hot" text (metadata-extracted) and caps cold CAS reads; early path/include filters.
  - Added a global time budget (internal) to stop long content scans gracefully.
  - Capped grep worker threads to a small, background-friendly number by default (≤4).
- Grep streaming optimization: replaced per-character streambuf overflow with bulk line splitting
  (memchr-based) to eliminate the per-byte hotspot in profiles during CAS streaming.
- Post-ingest queue: bounded by configuration, not CPU heuristics.
  - Default worker threads set conservatively to 1 unless configured in `[tuning]` as
    `post_ingest_threads`. Queue capacity now honored from `post_ingest_queue_max`.
  - Added a tiny yield between tasks to reduce contention and smooth CPU.
- Addressed intermittent CLI timeouts and “Broken pipe” logs observed when many agents
  connected concurrently. Accept loop backoff now respects the higher connection cap and IO pool
  growth from the tuning manager.
- Minor unit test fixes (Result<T> value handling) to unblock CI.