* refactor(tuning): prune dormant runtime knobs
Remove unused tuning controls and adaptive search budget state. Extract testable ONNX slot reconciliation and search telemetry hydration seams, and correct the Apple Silicon sysctl value width.
* refactor(vector): retire dormant backends
Remove unused FAISS, model-infrastructure, VectorIndexManager, and TurboQuant paths while keeping Simeon PQ and float-vector storage.
Migrate unused V2.2 quantized schemas transactionally to V2.3. Databases containing non-default quantized formats or packed-code blobs fail closed with recovery guidance and no mutation.
* refactor(plugins): remove legacy SDK tooling
Remove the Ghidra and SDK submodules, their bespoke tests, and stale scan exclusions. Retain generic PluginProcess coverage against the repository mock fixture.
* build(vector): remove stale FAISS overrides
* refactor(ipc): remove dormant FSM snapshots
* refactor(ingest): unify bounded KG enqueue
* fix(plugins): harden allocation contracts
Keep ABI outputs null or fully initialized when allocations fail, and represent empty object payloads without relying on malloc(0).
* fix(storage): define empty object reads
Return a null buffer with zero length for successful empty-object reads instead of treating malloc(0) as an allocation contract.
* refactor(storage): trim through string views
* test: prune dormant harness helpers
Remove unused readiness and fixture helpers, and keep benchmark client-count doubling in a wide integer domain.
* chore(cpp): initialize analyzer-facing locals
* build(simeon): advance analyzer cleanup
* refactor(config): drop dead daemon client keys
* refactor(ipc): inject daemon client transport
Socket and in-process execution now share DaemonClient request dispatch, so CLI fallbacks do not need alternate service paths.
* refactor(retrieval): route CLI through daemon
Search and grep now use the same daemon handlers over socket or in-process transport. Live grep remains an explicit freshness inspection.
* refactor(graph): move CLI scope into daemon
Graph CLI requests now share daemon handlers across socket and in-process transports. CWD filtering occurs before pagination so scoped totals and pages stay correct.
* build: isolate test-only runtime controls
* refactor(metadata): decouple lock telemetry
* fix(services): return on request timeout
* fix(retrieval): enforce workspace scope
* fix(graph): scope nodes before pagination
* fix(grep): drop binary result lines
* fix(daemon): bound checkpoint wait
* fix(repair): use KG health checks
* fix(storage): always verify compressed CRC
* perf(vector): skip unchanged PQ snapshots
* build(zyp): exclude bench from default build
* build: protect Meson files from formatter
* refactor: remove unreachable production APIs
* refactor(daemon): remove dormant runtime state
* fix(vector): harden daemon provider calls
Timed-out coroutines must own their client and requests. Provider discovery must also fail instead of returning synthetic embeddings in production.
* refactor(storage): remove unusable adapters
* fix(cli): unify in-process add requests
* fix(tsan): preserve async worker progress
* test(cli): isolate daemon-dependent suites
* fix(repair): expose queue backoff progress
* fix(release): repair package repo publish
Arch repo metadata and R2 uploads need to be reproducible from CI, with retry hardening for transient Cloudflare failures.
* fix(daemon): stop shutdown log storm
Init waiter must treat ShuttingDown as terminal so daemon shutdown tests do not flood Meson logs while the daemon is stopping.
* refactor(cli): delegate serve to MCP binary
Keep yams serve UX while removing MCP server linkage from yams-cli. The standalone MCP binary owns stdio serving and exits on stdin EOF.
* refactor(cli): move daemon path helpers
Keep CLI path resolution out of YamsDaemon so later link cuts can separate CLI and daemon internals. Full yams_daemon removal still needs a socket-only daemon-client split.
* refactor(daemon): split embedded client
* perf(search): add lean-guided benchmark gates
Add Lean topology/search models, ingestion ablation docs, and focused regression tests for topology and compression threshold behavior.
Extract search observability, keep benchmark-only ablation controls, and make retrieval quality benchmarks default to Simeon while preserving explicit ONNX opt-in.
* refactor(config): move daemon policies
* refactor(daemon): extract plugin runtime
* refactor(daemon): untangle service coordinators
Untangle CLI/MCP from daemon service coordinators and the daemon static lib.
- MetadataRepository uses a daemon-neutral tree-diff callback. The
GraphComponent wrapper moves to src/daemon/components/metadata_graph_bridge.cpp,
owned by the daemon library.
- WriteCoordinator moves to a dedicated build-only yams_write_coordinator
static lib. Drop ResourceGovernor coupling inside the writer loop; batch
sizing still respects config.maxBatchSize.
- AppContext gains enqueuePostIngest callback. ServiceManager wires it to
its own enqueuePostIngest; app services no longer call ServiceManager
directly.
- Embedding repair uses BulkIngestLease/BeginBulkIngestCallback instead of
concrete VectorIndexCoordinator::BulkScope. Daemon dispatchers provide a
lease factory backed by the real coordinator.
- CLI daemon_command uses config helpers instead of YamsDaemon::getXDGRuntimeDir.
- Remove explicit dependency('yams_daemon') from src/cli and tools/yams-mcp.
- Declare missing yams_extraction/yams_ingest deps on yams_app_services so
app services link cleanly without daemon.
Validated:
meson compile -C build/release -j4 yams-daemon yams-cli yams-mcp-server
ninja -C build/release -t commands tools/yams-cli/yams-cli tools/yams-mcp/yams-mcp-server | grep -c libyams_daemon.a -> 0
yams-cli --version, yams-mcp-server init, yams serve --help smoke tests
Size drop on macOS release: yams-cli 41M -> 32M, yams-mcp-server 37M -> 22M.
* fix(cli): keep stdin add local fallback
No embedded daemon now. When yams add - buffers stdin and daemon IPC is missing, store via local app services instead of failing socket_missing.
Validated:
meson compile -C build/debug -j4 yams-cli catch2_cli_commands
MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/debug build/debug/tests/catch2_cli_commands 'AddCommand - reads from piped stdin and stores content'
MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/debug build/debug/tests/catch2_cli_commands
meson compile -C build/release -j4 yams-cli yams-mcp-server
meson compile -C build/asan-api -j2 yams-cli catch2_cli_commands
MESON_BUILD_ROOT=/Users/trevon/work/tools/yams/build/asan-api ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 build/asan-api/tests/catch2_cli_commands 'AddCommand - reads from piped stdin and stores content'
ninja -C build/release -t commands tools/yams-cli/yams-cli tools/yams-mcp/yams-mcp-server | grep libyams_daemon.a -> no output
* feat(bench): add xplan multi-arm experiment harness
Unified plan runner, ablation axes, REPORT/ablation docs, and
KPI snapshot so optimization loops stop living in shell matrices.
* feat(formal): expand topology/search Lean contracts
Boundary models for search provenance, construction gates,
and cluster/route objectives so Lean guides correctness while
xplan ranks performance levers.
* feat(search,topology): construction purity + graph expansion path
Raise topology build defaults (min edge 0.25, max component 64) and
split oversized CC pieces so hybrid assist is quality-positive on
scifact. Add GraphNeighbors expansion with medoid-anchor fallback,
structured helpers instead of nested session logic, and BEIR-default
xplan plans. Search engine extraction (fanout/classic pipeline) rides
along as the integration surface for routing.
* feat(topology): add KMeans engine and SGC identity contracts
Register kmeans in the factory with deterministic spherical k-means
over embeddings, and enforce SGC document-identity invariants in
debug builds with matching unit coverage.
* feat(daemon): topology readiness gates and selectable reranker
Drive topologyReady from published epoch/freshness/rebuild/dirty
ingest state (not just KG drain), surface those fields in search
stats, and wire onnx|simeon|auto|none cross-reranker selection.
* chore(search): drop meta_path tuner knobs
Meta-path routing is gone; remove dead TunedParams fields and the
ConfigResolver test for [search.meta_path].
* feat(bench): add topology_purity_validate plan
Repeats=3 validation matrix for construction-purity winners vs
topo_off so MRR deltas can clear run-to-run noise.
* chore: format add_command and config include order
Mechanical clang-format / include reorder only; no behavior change.
* feat(bench): decision-grade xplan loop for search engine
Document search-engine measurement in AGENTS; harden xplan with
repeats=3 plans, quality×latency primaries, mechanism metrics from
debug.jsonl, multi-rep log promotion, and archive superseded topology
plans.
* feat(graph): denser product semantic_neighbor topK
Raise default YAMS_GRAPH_SEMANTIC_TOPK fallback from 4 to 8 so product
graphs leave fewer degree-0 docs for GraphNeighbors expansion.
* feat(search): extract topology assist and cross-rerank seams
Pull topology assist into search_topology_stage (seed merge, skip
reasons, optional vector seed probe default 0). Extract cross_rerank
compute from search_engine. Wire probe via typed config/ConfigResolver.
* feat(bench): product-path search engine ablation plans
Add topology-off component, vector-weight, and tiered-execution xplan
plans (repeats=3) and wire them into the AGENTS measurement loop table.
* fix(ci): repair pre-push fallbacks
* feat(bench): lock-free mid-run builds + multi-corpus gates
xplan skips meson rebuild when the quality binary exists (flock +
YAMS_BENCH_FORCE_BUILD override) to stop multi-arm link races. Add
graph_vector weight and nfcorpus transfer-gate plans; document in AGENTS.
* fix(daemon): keep SearchEngine alive via shared_ptr cache
getCachedEngine previously published a raw pointer that metrics polling
used through rebuild, racing destructor of SearchEngine::Impl (TSAN).
Store and return a shared_ptr snapshot so diagnostic readers pin the
engine for the duration of getConfig/health checks.
Also adds the cautious vectorWeight 0.30→0.20 multi-corpus xplan plan.
* feat(search): route vectors through cached topology
Build and reuse validated topology snapshots, rank routed members by query similarity, and narrow the vector leg to the accepted document set with explicit work diagnostics.
Remove the retired HDBSCAN engine and vendor dependency, preserve typed topology policy through search tuning, and cover the runtime/configuration contracts.
* feat(bench): consolidate search decision plans
Enforce deterministic experiment identity and declared baselines, expose routed/global vector work metrics, and register the focused benchmark contracts.
Promote the compact repeats=3 routing-budget gate, archive superseded topology mechanism screens, and add multi-corpus product calibration plans.
* feat(search): refine topology vector routing
* fix(search): propagate daemon readiness
* feat(bench): measure generalized memory health
* fix(cli): honor in-process fallbacks
* ci: harden smolvm debug builds
* perf(search): route topology through filtered ANN
* feat(bench): measure read-write pressure
* perf(metadata): index symbol lookups on read pool
* fix(daemon): isolate startup reads and maintenance
* feat(bench): replay isolated generalized corpora
* feat(search): add evidence routing pipeline
Replace the blocking smolvm pre-push path with host ASan/TSan validation, harden sanitizer-sensitive smoke tests, and add recovery cleanup for malformed SQLite WAL sidecars.
* refactor(search): unify topology evidence path
Remove classic and sidecar fusion lanes so topology augments the recall-preserving ANN and lexical candidate pool through one product path.
* refactor(bench): prune superseded search lanes
Measure the topology-plus-ANN product path with stable experiment identity and remove obsolete sidecar and tiered controls.
* docs(search): retire stale experiment notes
Keep the benchmark handoff focused on the topology-plus-ANN product lane and its active decision plans.
* refactor(search): prune dead search surfaces
Remove unused fusion, reranker, policy, and router abstractions.
Bound topology materialization and keep document trace payloads opt-in.
* fix(cli): clear build warnings
* fix(xplan): reject stale run identity
* refactor(search)!: remove legacy query stack
Replace the unused AST/ranker/post-processor surface with focused facet aggregation used by product search.
BREAKING CHANGE: removes query parser, result ranker, search filter, and SearchResults container APIs from yams_search.
* refactor(search): type value stage traces
Remove synthetic ComponentResult markers for embedding and concept stages. Preserve failure and timeout states instead of overwriting them with fake successful results.
* refactor(search): isolate benchmark env overlays
Move test-only search environment parsing behind an injectable internal adapter. Keep all existing overlay keys and tuner pin semantics while restoring SearchEngineBuilder to composition.
* refactor(search): unify topology routing options
Snapshot topology policy once at the assist boundary and pass it through routing sessions and diagnostics. Remove repeated scalar copying without changing routing behavior or metric keys.
* fix(search): unify tuner config ownership
Use one complete config-to-params overlay for runtime seeding and no-tuner policy resolution. Reseed attached tuners on setConfig so reported and executed configuration cannot diverge.
* fix(search): snapshot tuner state per query
Read tuned config, params, and state under one lock before routing. Add a TSAN correlation test so adaptive observation cannot produce a torn logical query snapshot.
* fix(search): enforce topology routing contract
Generated configs must preserve hybrid-assist shadow routing, while daemon-backed search must abstain when published topology artifacts are stale. Keep standalone validation and global ANN recall intact.
* fix(daemon): let SQLite reclaim its file
Directly resizing a live database from sampled page counts can truncate pages allocated by concurrent writers. VACUUM must remain the only file-reclamation mechanism.
* fix(metadata): tolerate missing symbol FTS
Readiness lookups can race an unavailable optional FTS migration. Retain the indexed fast path, but retry against the base table when prepare or cached-statement execution proves the capability absent.
* build(fuzz): drop removed query parser target
The optional AFL build still referenced the deleted legacy query parser API and could no longer compile.
* fix(bench): include writes in drain oracle
A zero post-ingest queue is not durable drain while coordinated writes remain queued or in flight.
* fix(daemon): vacuum padded WAL databases safely
- use real Python and Scoop executables under SSH and CI
- prefer python over python3 on Windows Meson probes
- keep forced socket mode pinned for both socket env names
- make forced-socket smoke test deterministic on Windows
- clean sqlite WAL/SHM sidecars and randomize temp DB names
- make video header parsing MSVC-safe and reject false MP4 hits
- give integrity_catch2 more time on Windows runners
* fix(core): add assertions and harden daemon lifecycle
* fix(daemon): tighten shutdown lifecycle invariants
* fix(test): add PressureLimitedPoller capability-sleep shutdown test
* refactor(vector): harden backend contracts
Split the vector backend surface into narrower contracts and
move entity read paths to Result<> so callers can distinguish
backend errors from empty results.
Also fixes the TurboQuant lazy-init race, makes VectorDatabase
error state thread-safe, wires eager index preparation, and
adds regression plus memory-scaling benchmark coverage.
* fix(vector): address audit findings plus hardening
Fix the five confirmed bugs: coroutine lifetime hazard in
embedding_generator (await_with_timeout outliving captured state),
VectorSystemManager init retry latch poisoning, incremental HNSW
persistence race, vec0 registry key collisions, and simeon PMI
output_dim/config() drift.
Add invariant hardening: PostIngestQueue stage validation +
numChunks assertion, VectorSystemManager success postcondition,
VectorDatabase TurboQuant non-null assertions on all quantize/
dequantize paths, and sqlite_vec_backend Simeon PQ range and
divisibility preconditions.
Also adds regression coverage for init-retry and lock-busy paths
and a locked node snapshot helper for safe incremental HNSW
persistence.
* fix(test): add PressureLimitedPoller wake-timer shutdown tests
* chore(vector): resolve clang-tidy hygiene across queue, vdb, and sqlite-vec
Replace unprotected std::getenv calls with locked getenvCopy helpers,
add debug-level logging to previously-silent catch blocks in
PostIngestQueue, VectorDatabase, and SqliteVecBackend, wrap
PostIngestQueue timer-detach allocations in try-catch, and fix
unsigned-widening / optional-deref / unused-include hygiene.
Verified with LSP diagnostics and rebuilds of catch2_vector_submodule
and catch2_daemon_component_submodule.
* fix(daemon): harden PressureLimitedPoller inFlightCounter null check
* fix(daemon): harden PostIngestQueue wait_until deadline checks
* fix(daemon): clean up recovery sentinels regardless of salvage count
Previously the .recovered-* sentinel and .corrupt-* file cleanup
was gated on documentsSalvaged > 0, leaving quarantine
artifacts to accumulate on repeated crash/recovery cycles where
the corrupt DB had 0 salvageable docs.
Move cleanup outside the salvage-count guard so stale
quarantine artifacts are always removed after examination.
* feat(vec0): restore persisted ANN index on daemon restart
After vec0 rebuild, probe for vectors_<dim>_hnsw_meta shadow tables
and load a previously-persisted HNSW index. When found, the ANN
index is set directly on the vec0 table, skipping the O(n log n)
rebuild that was previously paid on every daemon restart.
Removes the stub restoreVec0AnnIndexIfPresentUnlocked() in favor
of inline restoration in rebuildVec0DimUnlocked(), which has
the vec0 table already created and ready for ann_index assignment.
* fix: enable DCHECK by default and assert metadata counter consistency
* fix(services): assert document deletion ordering content-before-metadata
* fix(test): add fork-based assertion validation tests
* fix(test): expand assertion tests for POSTCONDITION, DCHECK, UNREACHABLE
* fix(ci): enable -Denable-dcheck=true in all test CI lanes
* fix(test): address assertion review findings
* refactor(daemon): isolate poller config assertion checks
* refactor(services): reduce deletion and poller complexity
* style(ci): normalize test workflow spacing
* refactor(services): extract list query helpers
* refactor(services): extract list hydration helpers
* refactor(daemon): extract metrics snapshot helpers
* refactor(daemon): extract metrics counter snapshot
* refactor(daemon): extract metrics resource snapshot
* feat(graph): add daemon-backed explore
Wire graph explore through daemon IPC, keep CLI rendering stable,
and fall back locally when daemon transport or protocol skew fails.
Also add graph context service/tests, improve graph follow-up hints,
and keep release builds working with the current JSON library.
* fix(services): prevent prune delete metadata orphans
* fix(cli): honor data-dir in graph explore
- bypass daemon explore when the CLI pins a data dir so\n temp fixtures do not resolve against a long-lived global DB\n- guard snippet truncation and ratio math to remove Fold-\n reported underflow and div-by-zero paths\n- clamp zero-based symbol lines before rendering graph\n context
* fix(daemon): make lifecycle stop completion safe
* fix(daemon): gate db-open startup against shutdown
* fix(metadata): serialize FTS indexed counter updates
* test(daemon): simulate vector lock contention cross-process
* test(daemon): isolate post-ingest identity batch
* style(daemon): normalize test include order
* refactor(graph): split cli graph helpers
Keep graph command paths smaller and easier to evolve.
Lock graph explore/topology contracts into focused presenter,
dispatcher, and support tests so follow-up refactors keep the
current IPC and hot-path behavior intact.
* fix(config): harden expand_tilde and fix Windows XDG state path doubling
- expand_tilde: handle bare ~ and ~/ explicitly to avoid std::out_of_range
on substr(2) for single-char input
- getXDGStateHome: on Windows, go up two levels from %LOCALAPPDATA%\yams\state
to %LOCALAPPDATA% so callers' xdg/yams append doesn't double the yams segment
* fix(static-analysis): add logging to empty catch blocks and fix nosemgrep syntax
* fix(static-analysis): strip trailing text from nosemgrep comments
* fix(doctor): add logging to daemon_check empty catch blocks
* fix(db_repair): add logging to empty catch blocks
* fix(chunking): add precondition checks for rabin polynomial and windowSize
* fix(safety): add null precondition checks for Fold proved null-deref sites
* fix(daemon): widen init-failure dispatch, add null/dbz preconditions
InitializationFailedEvent races with shutdown — async init
fails after teardown begins. Widen canDispatch to accept
Ready/ShuttingDown. Add static_assert on SnapshotRing N>0.
Add YAMS_PRECONDITION null guards on hex/stages/data/bytes.
* ci(ubsan): use restricted build targets to avoid runner timeout
* fix(daemon): detach wake timers on Windows stop path to prevent SIGSEGV
* fix(config): cast parseTomlU32 to size_t for batch fields
* fix(ci): use static helper for Windows timer leak, restrict ubsan tests
* test(storage): add crash-replay and handle-failure coverage for ReferenceCounter
Adds 6 test cases:
- Recovery after forced close preserves committed data
- Uncommitted transaction rolled back after forced close
- Corrupted database file rejected on open
- Consistent stats after interrupted commit recovery
- Multiple PENDING transactions survive force close
- WAL checkpoint survives forced close
* fix(ci): remove ccache — conflicts with OpenBLAS ASM as direct compiler
* fix(ci): use explicit CC/CXX paths to prevent Conan from using ccache directly
ccache was picked up by Conan/CMake as the compiler itself (/usr/bin/ccache)
rather than as a transparent wrapper, causing OpenBLAS ASM compilation to fail
with 'ccache: invalid option -- D'. Setting explicit compiler paths prevents this.
* fix(ci): add YAMS_SKIP_CCACHE to avoid OpenBLAS ASM ccache conflict
setup.sh wraps CC/CXX with ccache for faster incremental builds, but
this causes Conan/CMake to use ccache directly as the ASM compiler for
OpenBLAS, where it fails on -D flags. Add an opt-out gate in setup.sh
and set YAMS_SKIP_CCACHE=1 in .build.yml for sourcehut CI VMs.
* fix(ci): add libomp-dev, libfaiss-dev, libopenblas-dev for FAISS build
* fix(ci): limit meson compile to -j1 to prevent OOM on sourcehut VMs
* fix(build): restore hooks and shrink srht
Compile the storage library with YAMS_TESTING in test builds so
debug-only hooks link again.
Include the POSIX chmod header used by the storage utility
Catch2 coverage cases.
Prune SourceHut fallback stage archives to runtime files so
branch artifacts stay under the upload limit.
* refactor(storage): drop dead code, add coverage
* refactor(cli): polish grep/search graph UX
* fix(daemon): stabilize shutdown and CI paths
- force vector-backed tests to opt out of CI-wide disable flags
- reset reference prune statements between deletes
- make optional-plugin and POSIX-only test assumptions portable
- extract ServiceManager open/shutdown helpers for safer WAL recovery work
* test(daemon): add db vacuum coverage
* test(daemon): add WAL startup recovery
- cover stale WAL startup recovery in ServiceManager
- cover repeated restart cycles with seeded WAL sidecars
- assert daemon recovery reporting for corrupt data-dir DBs
- verify oversized metadata DBs shrink after WAL recovery shutdown
* refactor(grep): consolidate indexed content scan
* fix(grep): remove pre-scan candidate truncation
* refactor(runtime): split startup, harden storage
* feat(bench): add manifest retrieval corpus
* fix(bench): run fusion experiment on simeon
* fix(cli): sharpen search graph hints
* fix(build): refresh version metadata
* fix(ci): stabilize sync search and srht packaging
* fix(ci): unblock windows and shrink artifacts
* fix(ci): stabilize linux runtime checks
* fix(build): shrink srht manifest
