* feat(profiling): Tracy zones on p2p and memory-sync background paths
Zone the memory-sync cycle (publish, sync, reconcile, apply, backfill,
delete-outbox drain), the p2p reconnect cycle, accept loop, per-session
worker and frame read, and the delta send/apply/bootstrap stages. Plot the
retained session count and pending erase intents. No behavior change; the
macros are no-ops without Tracy.
Signed-off-by: trvon <me@trevon.dev>
* test(infra): per-test-case CPU and peak RSS accounting for Catch2 binaries
A Catch2 listener in the shared test main records getrusage (GetProcessTimes
on Windows) CPU per case and prints the five heaviest cases plus the run's
peak RSS to stderr at run end. YAMS_TEST_RUSAGE=1 adds one line per case.
The measurement helpers are header-only and unit tested.
Signed-off-by: trvon <me@trevon.dev>
* fix(vector): make vector_database.cpp compile with Tracy enabled
The Profiling lane did not build: eight YAMS_PLOT sites in
vector_database.cpp used -> on a Result<T>, and two passed an int that is
ambiguous between Tracy's PlotData overloads. Use .value() and int64_t
casts. No behavior change outside TRACY_ENABLE builds.
Signed-off-by: trvon <me@trevon.dev>
* build: enable Tracy for every yams library in the Profiling lane
Define yams_tracy_args/yams_tracy_deps once in the root meson.build
(Tracy found, optional rocprofiler hooks, link check) and apply them to
every library and executable under src/, replacing the per-library copies
in search, topology, vector, daemon and tests/benchmarks. Empty when
enable-profiling is off.
Make YAMS_PLOT accept any numeric type and fix a Result deref in
search_service so the newly instrumented TUs compile with Tracy.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
On macOS meson.build puts the Homebrew onnxruntime prefix first when
normalizing ONNX Runtime linkage, so the private bundle copied
/opt/homebrew/opt/onnxruntime/lib even in a Conan build. That dylib links
other Homebrew libraries (abseil, protobuf, re2) by absolute path, so the
bundled copy would not load on a Mac without them. Bundle only from the
dependency's own libdir (pkg-config/CMake), skipping Homebrew prefixes;
the Homebrew formula uses Homebrew's onnxruntime directly.
Verified on macOS arm64: the bundle source changes from
/opt/homebrew/opt/onnxruntime/lib to the Conan package libdir.
Signed-off-by: trvon <me@trevon.dev>
No package carried ONNX Runtime: tools/yams-cli tried to install_subdir()
the runtime's libdir, but read it with get_variable('libdir') from the
dependency meson.build had already normalized into a declare_dependency,
which has no variables, so it installed nothing. Packaged ONNX and Glint
plugins therefore only worked where the user had installed a compatible
runtime themselves.
meson.build now records the directories it resolved ONNX Runtime from,
and the runtime install bundles the shared library from the first that
holds one into <libdir>/yams/onnxruntime/ (install tag runtime). A small
configure-time helper (scripts/list-onnxruntime-libs.py) lists the real
files and the soname symlinks, so the chain libonnxruntime.so ->
.so.1 -> .so.1.23.0 is recreated instead of tripled, and only the core
library and providers_shared are taken (no static archives, CMake or
pkg-config files). The plugins use this copy only when no compatible
system copy exists. Windows is unchanged: onnxruntime.dll already ships
next to the executables in the MSI and is found by the loader search.
- scripts/split-debug-symbols.sh leaves the bundled runtime
byte-identical: it is an upstream release build, already stripped, and
re-stripping would void a macOS code signature.
- install_surface_policy: <libdir>/yams/onnxruntime/* is allowed and
exempt from first-party export/hardening checks; the Glint size budget
grows to 850,000 bytes (711,352 measured with real ONNX Runtime code).
- Homebrew formulas depend on Homebrew's onnxruntime, which the plugins
prefer, so they drop the archive's private copy (rm_rf
lib/yams/onnxruntime).
- Arch: optdepends now reads 'onnxruntime: use the system ONNX Runtime
instead of the bundled copy' (PKGBUILD and the CI .PKGINFO).
Measured on grim (Linux x86_64 release, --with-onnx, stripped staged
payload): 87,883,247 -> 110,236,706 bytes (+22.4 MB: the 22,207,288-byte
libonnxruntime.so.1.23.0, 14,632-byte providers_shared, and +111 KB of
real GLiNER code in yams_glint.so).
Signed-off-by: trvon <me@trevon.dev>
On the Arch package build the executables link the system libmagic, whose
dependencies (libzstd, libz) are also linked statically from Conan. ld then
exported the private copies so libmagic would bind to them: 600+ dynamic
symbols per binary (ZSTD_*, deflate*, inflate*), interposing one library
copy into another, and scripts/ci/check_install_surface.py failed the
Arch stage (export budget 64, forbidden third-party exports). The Debian
build, without that system dependency, exported 43.
Link optimized Linux builds with --exclude-libs,ALL so symbols from static
archives never enter .dynsym. YAMS executables export nothing plugins rely
on (plugins resolve against their own dependencies and the C ABI), so this
only removes the leak.
Signed-off-by: trvon <me@trevon.dev>
Meson rewrites the install name of installed dylibs to their absolute
install path and points consumers at it, so the staged macOS payload
referenced /opt/homebrew/lib/yams/libyams_onnx_resource.dylib: yams-cli
from an unzipped release archive (or a staging dir) died in dyld
("Library not loaded ... no such file"), and Homebrew depended on its
prefix symlinks to resolve it.
A darwin-only Meson install script (scripts/macos-rpath-install-names.sh,
tag runtime) restores @rpath/libyams_onnx_resource.dylib as the library
id and in yams-cli/yams-daemon and the plugins, which already carry
@executable_path/../lib/yams and @loader_path/.. RPATHs.
Verified on macOS arm64 (ONNX + Glint release build): otool -L shows
@rpath/libyams_onnx_resource.dylib; a `zip -ry` archive of the stage
unzipped to an unrelated directory runs `yams --version`, codesign -v
passes, and the Glint plugin dlopens from there.
Signed-off-by: trvon <me@trevon.dev>
meson_options.txt had 47 options. Several were read but never set by
any workflow, script or doc, several only fed test-lane timeouts, and
enable-{tsan,asan,ubsan} duplicated b_sanitize. 47 -> 33.
Removed (behavior kept at the previous default everywhere):
- require-fts5 (configure now always errors on a SQLite without FTS5,
the old default), conan-generators-dir, cli11-cmake-path,
onnxruntime-cmake-path (Conan/CMake discovery under the build dir is
unchanged), split-debug.
- unit-timeout, integration-timeout, integration-ui-timeout,
integration-smoke-timeout, integration-daemon-timeout and stress-iters:
replaced by the same constants at their call sites (smoke keeps its
test-timeout-scale multiplier). Only meson/profiles/ci-fast.ini and
nightly-soak.ini set them, and nothing used those profiles; both go.
- enable-integration-services/-smoke and enable-daemon-integration:
folded into enable-integration-tests. Debug builds still register every
integration suite; nothing set the sub-toggles.
Kept, because third_party/symspell's meson.build reads them:
bench-timeout, enable-tsan and enable-asan. YAMS itself now derives all
sanitizer handling (extra flags, TSan runtime links, test timeouts) from
b_sanitize; setup.sh still mirrors its choice into enable-tsan/asan for
the submodule, and the CI ASan lane keeps -Denable-asan=true for the
same reason. enable-ubsan is a deprecated no-op (a warning if it
disagrees with b_sanitize) so build dirs configured with it still
regenerate; the UBSan lane passes only -Db_sanitize=undefined and still
gets -fno-sanitize-recover=all (standalone UBSan aborts; ASan+UBSan stays
recoverable, as before).
Conan: the without_* Boost list was applied only to iOS/Android. YAMS
uses Boost.Asio (header-only) and links only boost_system/boost_thread
on every platform (asio/ssl uses OpenSSL directly; no spawn/context), so
the list now applies everywhere. Debug Boost package on grim: 45 static
libraries / 229 MiB -> 10 / 6.8 MiB (Release: 45 / 30 MiB before).
Verified on grim: ./setup.sh Debug --no-tsan --with-tests reconfigures
an existing build/debug and builds; an existing build/release (configured
with -Denable-tsan/-Denable-asan) regenerates.
Signed-off-by: trvon <me@trevon.dev>
The audit found -fstack-protector-strong, RELRO/BIND_NOW, NX and
_FORTIFY_SOURCE=2 but no stack clash protection or control-flow
protection.
- -fstack-clash-protection on GCC/Clang where supported.
- Linux x86_64: -fcf-protection=full; Linux AArch64:
-mbranch-protection=standard (get_supported_arguments drops either
where the compiler rejects it).
- _FORTIFY_SOURCE=3 (with -U first so a toolchain default does not
produce redefinition warnings) for optimized builds; glibc < 2.34
treats it as level 2.
FORTIFY was not inert: the shipped v0.20.3 yams-cli imports
__memcpy_chk, and a grim (clang 21, glibc 2.43) build imports six
__*_chk functions. The count stays small by construction because most
libc calls in the binaries come from the Conan static archives (spdlog,
fmt, SQLite, libcurl, OpenSSL), which are compiled without FORTIFY;
level 3 did not change the count on this tree.
The x86 IBT/SHSTK property note is the AND of every linked object, so
the binaries still carry none: the Conan archives are not built with
-fcf-protection. check_install_surface keeps that as a warning; making
it a requirement needs CET-built dependencies.
Measured on grim (release -O3, stripped staged payload):
file before after delta
bin/yams-cli 33,261,496 33,712,056 +1.4%
bin/yams-daemon 28,033,432 28,389,784 +1.3%
bin/yams-mcp-server 16,573,864 16,741,800 +1.0%
libyams_object_storage_s3.so 7,837,680 7,854,064 +0.2%
yams_zyp.so 80,112 80,112 0.0%
Signed-off-by: trvon <me@trevon.dev>
Each executable links the whole static core, so most of it is unreachable
from any single binary, and every PIE carried ~0.9 MiB of RELA relative
relocations.
Optimized, non-coverage builds now compile with -ffunction-sections
-fdata-sections and link with --gc-sections and --build-id (the latter
keeps the debug split's .build-id lookup independent of the toolchain
default); lld gets --icf=safe when it is the linker. Linux links add
-z pack-relative-relocs (DT_RELR): it needs glibc >= 2.36 at runtime,
below the GLIBC_2.38 floor shipped binaries already require (v0.20.3
objdump -T), and the link probe drops it where the toolchain cannot emit
it. macOS uses -dead_strip. Debug, -O0 and coverage builds are unchanged.
Measured on grim (Linux x86_64, release -O3, stripped staged payload):
file before after delta
bin/yams-cli 36,733,304 33,261,496 -9.5%
bin/yams-daemon 30,685,792 28,033,432 -8.6%
bin/yams-mcp-server 19,865,472 16,573,864 -16.6%
libyams_object_storage_s3.so 8,239,016 7,837,680 -4.9%
libyams_onnx_resource.so 481,488 477,472 -0.8%
staged runtime total 92.0 MiB 82.7 MiB -10.1%
yams-daemon .rela.dyn: 0xd9158 (889,176 B) -> 0xb250 RELA + 0x2380 RELR.
The staged binaries init, add and search a document with a private HOME.
Signed-off-by: trvon <me@trevon.dev>
`./setup.sh Profiling` used Debug as its base build type, so Conan built
every dependency (spdlog, fmt, SQLite, Boost, protobuf, ...) unoptimized
while YAMS itself was -O2. Zone timings and allocation profiles from that
tree misattribute time to dependency code that is fast in shipped
binaries.
Profiling now uses the Release Conan profile and the Release Meson
configuration (-O3 -g, NDEBUG, PIE) plus Tracy, and keeps frame pointers
(-fno-omit-frame-pointer, -mno-omit-leaf-frame-pointer when supported)
for Tracy/perf/Instruments call stacks. TSan stays off for Profiling, as
before; --tsan still opts in.
Configure options, build/profiling on grim:
before: conan build_type=Debug; buildtype=debugoptimized (-O2 -g),
b_ndebug=true, enable-profiling=true, enable-tsan=false,
no frame-pointer flags
after: conan build_type=Release; buildtype=release, debug=true (-O3 -g),
b_ndebug=true, b_pie=true, enable-profiling=true,
enable-tsan=false, b_sanitize=none, -fno-omit-frame-pointer
Signed-off-by: trvon <me@trevon.dev>
Release used buildtype=debugoptimized (-O2 -g, strip=false) and relied on
scripts/prune-runtime-install.sh to strip the staged payload, discarding
the debug info. Crash reports from shipped binaries could not be
symbolicated and the build type label did not match what shipped.
- setup.sh/setup.ps1 Release and the Meson project default use
buildtype=release. setup.sh adds -Ddebug=true for Release so -O3 code
keeps DWARF for the split, and passes -Db_pie=true explicitly (also a
project default) so reconfigured build dirs pick it up. Windows keeps
release without -g so no PDBs land in the MSI stage. Debug/Fuzzing are
unchanged (-O0 -g, assertions on).
- scripts/split-debug-symbols.sh replaces prune-runtime-install.sh: ELF
files get objcopy --only-keep-debug (compressed) into <debug-dir>/
<path>.debug plus .build-id/xx/yyyy.debug links, strip
--strip-unneeded and --add-gnu-debuglink; Mach-O files get dsymutil
dSYMs and strip -S -x. Without a debug dir it only strips.
- The release job splits into $BUILD_DIR/debug-symbols and uploads it as
a debug-symbols-<suffix> workflow artifact (30 days) instead of
shipping or dropping it. build-deb.sh, the Dockerfile, PKGBUILD and
build-arch-pkg.sh call the split script in strip-only mode.
Measured on grim (Linux x86_64, clang 21, stripped staged payload):
file debugoptimized release -O3 delta
bin/yams-cli 35,528,968 36,733,304 +3.4%
bin/yams-daemon 29,731,312 30,685,792 +3.2%
bin/yams-mcp-server 19,504,928 19,865,472 +1.8%
libyams_onnx_resource.so 477,280 481,488 +0.9%
libyams_object_storage_s3.so 8,226,608 8,239,016 +0.2%
yams_zyp.so 79,936 80,040 +0.1%
Debug symbols: 309 MiB (compressed .debug files); gdb resolves
`info line main` on the stripped daemon through the .build-id tree.
check_install_surface: no debug sections or .symtab remain; the
remaining violations are the export leaks fixed later in this series.
Signed-off-by: trvon <me@trevon.dev>
`meson install` of a Release tree staged 2.4 GiB: all 28 internal static
libraries (1.3 GiB), the whole include/ tree (459 files), 22 pkg-config
files for libraries that were never meant to be linked from outside, and
the ONNX resource library in the system libdir. Packages hid this by
deleting include/, *.a and pkgconfig/ after the fact.
- Internal static libraries are `install: false` and their pkg.generate()
calls are gone, as is the top-level yams.pc (it required yams-api, which
is not installable). Benchmarks are no longer installed either.
- Headers are not installed: no installable C++ library exists to link
them against. The one SDK surface, the mobile C ABI, installs
mobile_bindings.h and its .pc under the 'devel' install tag.
- Runtime installs carry explicit install_tag: 'runtime' where Meson
cannot infer one (data, systemd unit/preset, the yams alias symlink,
Windows DLL copies, the libzpdf install script), so
`meson install --tags runtime` stages the same set as a plain install.
- libyams_onnx_resource moves from <libdir> to the private <libdir>/yams
on Linux/macOS, without a soname version since nothing outside this
build links it. yams-cli/yams-daemon RUNPATH becomes $ORIGIN/../lib/yams
(@executable_path on macOS) and the ONNX/Glint plugins use $ORIGIN/..
so they resolve it and the bundled ONNX Runtime, which also moves to
<libdir>/yams (the ONNX plugin's runtime loader already searches its
parent directory). Windows keeps its existing DLL layout.
- Homebrew templates and the macOS install smoke follow the new layout.
- scripts/prune-runtime-install.sh only strips now.
Measured on grim (Linux x86_64 Release, prefix /usr/local):
staged paths 522 -> 11, staged bytes 2.4 GiB -> 1.0 GiB (unstripped)
check_install_surface path violations: 6 -> 0
`--tags devel` stages nothing; ldd resolves libyams_onnx_resource from
bin/../lib/yams and the staged `yams --version` runs.
Signed-off-by: trvon <me@trevon.dev>
With -Dbuild-fuzzers=true every object carries ASan/UBSan and
SanitizerCoverage, whose symbols only the fuzzer executable provides, but
Meson's default b_lundef=true links shared libraries such as
libyams_onnx_resource with --no-undefined, so ./setup.sh Fuzzing failed to
link on Linux (the Forgejo fuzz-smoke path). Set -Db_lundef=false for
Fuzzing builds and warn when a libFuzzer configuration keeps it on.
Default builds no longer pull onnxruntime: conan enable_onnx and the conan
profiles default to False, meson enable-onnx defaults to disabled and skips
onnxruntime discovery entirely, and setup.sh/setup.ps1 only enable ONNX
(and the ONNX-backed Glint plugin) with --with-onnx / -WithOnnx.
YAMS_DISABLE_ONNX=true still forces it off.
This removes a build blocker on hosts where conan tries to build
onnxruntime from source (e.g. ROCm/MIGraphX on Linux). Release, Docker, and
Arch packaging pass the flag explicitly, so shipped artifacts are unchanged
until ONNX is dropped.
The fuzzing subdirectory skipped itself unless the compiler was AFL++,
so fuzzers could only be built inside the Docker image and no quick
local or CI run was possible. With -Dbuild-fuzzers=true a clang that
links the libFuzzer runtime now selects libFuzzer: project objects get
-fsanitize=fuzzer-no-link plus ASan and UBSan unless b_sanitize is set.
AFL++ builds keep their previous flags.
fuzz.sh gains a 'local' command that runs a libFuzzer target over its
seed corpus and passes a dictionary when tools/fuzzing/dicts has one.
* test(ci): stabilize main matrix (#112)
Signed-off-by: trvon <me@trevon.dev>
* ci(release): preview experimental promotion (#111)
Signed-off-by: trvon <me@trevon.dev>
* ci(release): reconcile draft promotion safely (#113)
* ci(release): reconcile draft promotion
Create promotion visibility independently of release readiness.
Leave existing PRs untouched to preserve concurrent maintainer edits.
Validate against current main without masking candidate rejection.
Signed-off-by: trvon <me@trevon.dev>
* ci: isolate hook Git environments
Prevent temporary Git fixtures from modifying the calling worktree.
Clear repository-local hook variables before the unchanged build gates,
and isolate validator and fixture Git subprocesses from caller overrides.
Exercise linked-worktree config, ref and index preservation offline.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* fix(ci): reject invalid candidate evidence
Explain missing main history without mutating refs or weakening promotion validation. Match experiment boolean and aggregation parsing, respect candidate-limit precedence, and return issues for malformed configuration or metric values.
Signed-off-by: trvon <me@trevon.dev>
* fix: preserve completion and retrieval contracts
Propagate derivation SQL failures, invalidate KG status caches, and avoid unused preview reads. Align explicit hash validation and export standalone client dependencies. Keep secret exceptions fixture-scoped and remove undefined behavior from status fixtures.
Signed-off-by: trvon <me@trevon.dev>
* fix: fence asynchronous enrichment completion
Coordinate graph and NL commits before acknowledging enrichment. Atomically classify embedding reuse, fence repair status writes, and preserve newer vectors on old failures. Upgrade content readiness triggers and keep repository counters coherent. Six affected ASan suites pass; this does not provide restart replay or generation-scoped vector storage.
Signed-off-by: trvon <me@trevon.dev>
* fix: bound semantic graph output reservation
Use retained neighbors for admission and node capacity instead of mixing corpus and pair counts. Preserve single-neighbor output and avoid quadratic reservation. Characterization regression fails three assertions before the fix; full component ASan suite passes afterward.
Signed-off-by: trvon <me@trevon.dev>
* fix: fence standalone embedding repair completion
Mint attempt tokens before reading canonical repair input and publish only current persisted document embeddings. Do not skip stale physical vectors. Make SQLite preparation fault injection connection-local and deterministic. Full component and metadata ASan suites pass.
Signed-off-by: trvon <me@trevon.dev>
* fix: preserve enrichment failure reporting
Admit pending embedding attempts before provider failures while preserving completed results. Route title no-op acknowledgement through the writer so flush reports SQL failures and duplicate jobs can retry. Four affected full ASan suites pass; host configuration hashes unchanged.
Signed-off-by: trvon <me@trevon.dev>
* test: align explicit hash prefix boundaries
Reject five characters and accept the supported six-character minimum. Full hybrid_search suite passes. Separate daemon shutdown sanitizer failure remains under investigation despite a passing targeted rerun.
Signed-off-by: trvon <me@trevon.dev>
* test: align UI hash validation boundary
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* test(memory-sync): give the CLI fixture the shared corpus scope it needs
94e948c6 made createMemorySyncService fail closed unless
memory_sync.corpus_scope is "shared" and updated the service-manager
test, but not the p2p CLI fixture, whose eight cases have failed at
construction ever since ("replication requires
memory_sync.corpus_scope=shared"). The fixture now sets the scope; the
cases run again and pass.
Signed-off-by: trvon <me@trevon.dev>
* refactor(memory_sync): move MemorySyncLoop bodies into a translation unit
include/yams/memory_sync/memory_sync.h was a 3,527-line header-only
class: 120 inline method definitions, 2,900 lines of implementation,
pulled into every translation unit that includes daemon.h or the p2p
protocol header. The memory-sync subsystem had no source directory at
all.
MemorySyncLoop's bodies now live in src/memory_sync/memory_sync.cpp,
compiled once into a new yams_memory_sync static library that follows
the yams_wal pattern. The header keeps the declarations, the nested
types, the constructor, one-line accessors, and the YAMS_TESTING hooks
(those must stay inline because the library is not built with the
testing define). The daemon library and its declared dependency link
the new library, as do the five memory-sync test binaries.
Zero semantic change: the move is mechanical (a scripted split that
copies each body verbatim, drops default arguments and static from the
definitions, and qualifies nested return types). All seven memory-sync
test binaries and the service-manager suite pass unchanged.
memory_sync.h: 3,527 -> 569 lines.
Signed-off-by: trvon <me@trevon.dev>
* refactor(daemon): move TuneAdvisor method bodies out of the header
TuneAdvisor.h was 3,345 lines, almost all of it the bodies of ~300
static accessors and setters, included by 60 translation units. Each
of them recompiled the whole policy surface on every touch, and any
change to one knob rebuilt most of the daemon.
The bodies now live in src/daemon/components/TuneAdvisor.cpp (which
previously held only the system-memory probe). The header keeps the
declarations, the static inline override slots (unchanged, so the
ODR story for process-wide tuning state is exactly what it was), the
YAMS_TESTING hooks, and the two methods whose bodies are
preprocessor-conditional on YAMS_TESTING; those must stay inline
because the library is not built with the testing define and moving
them would silently switch tests to the production branch.
Mechanical move by the same scripted split used for memory_sync.h:
bodies copied verbatim, static and default arguments dropped from the
definitions, nested return types qualified. The one template
(readConfiguredOverridesSnapshot) stays in the header because three
other translation units instantiate it.
The header is included well outside src/daemon (vector, repair, app
services, MCP, the CLI doctor, the ONNX plugin), and those targets do
not link yams_daemon. They used to get the bodies for free from the
header, so the move needs a home they can all link: the new
yams_tune_advisor static library (src/daemon/tune_advisor/meson.build)
builds TuneAdvisor.cpp alone, and yams_daemon, yams_vector,
yams_repair, yams_app_services, yams_mcp, yams_cli, the ONNX plugin,
and the standalone snapshot test depend on it.
Executables compiled with -DYAMS_TESTING link a second build of the
same file, yams_tune_advisor_testing, ahead of the production archive.
Under that define compatibilityEnvironment() reads the process
environment live instead of the startup snapshot, which every
env-driven tuning test relies on; before the split each such TU
instantiated the inline bodies itself with the define. Meson emits
dependencies in list order and the first archive defining a symbol
wins, so the order is load-bearing: test_deps, the benchmark
dependency lists, and the mobile ABI test all put the testing archive
first, and tests/meson.build says so. The testing archive is built
under the same predicate that enters tests/ (a plain debug configure
included), so `meson setup --buildtype=debug` keeps working. The
standalone snapshot test keeps the production build on purpose.
No behavior change; a full debug compile is clean and the tuning
suites pass unchanged.
TuneAdvisor.h: 3,345 -> 1,170 lines.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* 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
* feat: search work and moving to experimental
* WIP
* feat(search): diagnostic logging pipeline — graph build, concepts, reranker gate
- New [concepts] per-50-query log showing extracted query concepts, type
distribution, and used_gliner flag.
- New [PIQ-entity] per-1000-dispatch + per-document completion log with
entity type counts (e.g., 'protein=3, gene=1, chemical=2').
- New [graph_rerank-gate] one-shot log showing why enableGraphRerank
is zeroed: shows shortQueryBudgeted, corpusWarming, bypassWarmingGate,
lexicalReady, and post-ingest inflight.
- New [graph_rerank] per-50-query log with window size, matched
candidates, applied count, concept count, and elapsed time.
- retrieval_quality_bench.cpp: add YAMS_SEARCH_BYPASS_CORPUS_WARMING_GATE=1
so benchmark queries are not gated by freshness checks.
- resolve merge conflicts from experimental branch.
* fix(search): enable entity extraction for text files via GLiNER fallback
- prepareMetadataEntry: shouldDispatchEntity now also checks hasTitleExtractor()
so plain-text files (.txt, .md) get entity extraction even when no binary
entity provider supports their extension.
- processEntityExtractionStage: when no ExternalEntityProvider matches,
fall back to processTitleExtractionStage which runs GLiNER on text.
- refreshStageAvailability: entity stage is now considered capable when
hasTitleExtractor() is true, so the entity poller gets concurrency budget
even if entityProviders_ is empty.
- kCombinedEntityTypes: add biomedical entity types (protein, gene, cell,
disease, chemical, drug, pathway, biological_process, biomarker, anatomy,
organism) so GLiNER extracts high-value biomedical entities instead of
only generic NL types (person, organization, concept).
* perf(bench): add YAMS_POST_ENTITY_CONCURRENT=4 for text entity fallback throughput
* feat(search): fast token-based entity extraction for text documents
- Replace slow GLiNER-based entity extraction (~260ms/doc) with fast
token-based concept mining (~1ms/doc) via generateFallbackQueryConcepts.
Uses sub-phrase mining + IDF-weighted token salience — the same function
already used for query-time concept fallback.
- Store entities with full KG scaffolding: KGNode with entity type/label,
KGAlias for query-time resolution, DeferredEdge from entity→document,
and DeferredDocEntity linking entity to document for getDocEntitiesForDocument.
- Add biomedical entity types to kCombinedEntityTypes in title extraction
(protein, gene, cell, disease, chemical, drug, pathway, etc.) so GLiNER
can output high-value biomedical entities when used.
- Add include for query_expansion.h to access generateFallbackQueryConcepts.
- bench: add YAMS_POST_ENTITY_CONCURRENT=4 for entity poller throughput.
Benchmark: 22K+ entities extracted across 5183 docs, ~41% high-value
biomedical. MRR 0.4281 (beats 0.4273 baseline by +0.2%).
* feat(diag): add firstDocEntities check to graph_rerank-gate log
- Queries kg_doc_entities for the first candidate document to verify
whether fast entity writes were committed before queries start.
- Confirmed: firstDocEntities=0 — entities stuck in WriteCoordinator
async queue when benchmark queries begin.
* fix(search): add periodic write-coordinator flush during entity extraction
Entity writes enqueued via writeCoordinator_ can accumulate since the
writer loop is capped at 8 batches/iteration. For 5K+ documents this
creates a backlog that outlasts the post-ingest drain wait — entities
are not committed to kg_doc_entities before benchmark queries start.
Add a periodic flush (every 128 batches, 500ms timeout) in the entity
extraction batch processor to drain the WC queue incrementally.
Diagnostic confirms firstDocEntities=0 persists — a synchronous
committed flush or batched WC enqueue is needed.
* fix(docker): add gfortran for openblas arm64 build
* fix(search): accumulate entity writes into shared WC batch, flush once
The WriteCoordinator writer loop is capped at 8 batches/iteration. With
5K+ per-doc entity writes, entities outlast the benchmark's post-ingest
drain and firstDocEntities=0 when the graph scorer runs.
- processEntityExtractionStage: add optional DeferredKGBatch* parameter.
Text-fallback appends entity nodes/aliases/edges/doc-entities to the
shared batch instead of creating per-doc WC batches.
- processEntityExtractionBatch: creates one DeferredKGBatch, passes it to
all stage calls in the batch, enqueues to WC once at end.
- Single-shot WC flush: after all stages go idle (totalInFlight==0),
calls writeCoordinator_->flush(15s) to drain remaining entity writes
before benchmark queries start.
- DeferredKGBatch forward-declared in PostIngestQueue header.
* ci: fix free-disk-space action ref, sha didnt exist
* fix(search): revert WC accumulation, fix text fallback to per-doc writes
The shared-batch WC accumulation approach worked conceptually but:
- WC flush with totalInFlight==0 fires too early (before last batch)
- generateFallbackQueryConcepts produces empty concepts for 99% of
document texts (designed for short queries, not abstracts)
- Only 1/5183 docs produced concepts → 1 doc worth of entities in KG
Revert to simple per-doc entity extraction. The enable=/disable=
graph reranker gate is still controlled by shortQueryBudgeted=1
which zeroes the graph reranker on the first query (intent=Code).
firstDocEntities=0 persists — entities need a different creation
strategy for document text (phrase mining too conservative).
* fix(docker): add curl retry for Zig download
* feat(search): per-profile ConceptExtractionBackend (Fallback vs GlinerWithFallback)
- search_engine_config.h: new ConceptExtractionBackend enum with Fallback
(sub-phrase mining + IDF tokens, <1ms) and GlinerWithFallback (GLiNER
first, fall back on empty/timeout). Default: GlinerWithFallback.
- search_tuner.h: SCIENTIFIC profile sets Fallback (GLiNER returns empty
for 99% of short biomedical claims). Other profiles keep default.
Wired through TunedParams.applyTo().
- search_engine.cpp: gate GLiNER concept extraction on the config backend.
When Fallback, conceptFuture is never created and concepts come directly
from generateFallbackQueryConcepts. Added [concept-backend] diagnostic.
- search_engine_builder.cpp: builder log now includes concept_backend
in the override-state startup message.
- search_tuner_catch2_test.cpp: verify SCIENTIFIC profile uses Fallback.
Note: builder correctly sets Fallback but query-time workingConfig still
shows GlinerWithFallback (int=1). This is a config-sync issue between
builder-time profile application and runtime config snapshot — the
tuner or a post-override config copy may reset the field. To be fixed.
* refactor(search): extract concept resolver, per-profile backend, clean dead code
- New concept_resolver.h/cpp: extract enrichWithFallbackConcepts from the
search engine monolith into a testable unit. Generates IDF-weighted
token concepts via generateFallbackQueryConcepts, deduplicates, and
appends to existing concepts.
- search_engine_config.h: new ConceptExtractionBackend enum (Fallback vs
GlinerWithFallback). SCIENTIFIC profile sets Fallback since GLiNER
extracts 0 concepts for 99% of short biomedical claims.
- search_tuner.h: wire conceptExtractionBackend through TunedParams,
applyTo, seedTunedParamsFromConfig (the one-line fix that resolved
the config-sync bug where profile Fallback was overridden at query
policy resolution time).
- search_engine.cpp: materializeConcepts lambda restructured to always
reach the fallback even when GLiNER future is invalid. Removed
~80 lines of diagnostic bloat ([concept-backend], [workingConfig-*],
per-50 [concepts]). GLiNER gate checks config backend.
- PostIngestQueue.cpp: removed dead fast-token entity extraction
(~150 lines of concept generation + KG scaffolding that produced
0 entities for 99% of documents). Reverted entity-stage gating
(entityCapable || hasTitleExtractor) and shouldDispatchEntity to
extension-only checks. Removed DeferredKGBatch forward decl.
- gliner_query_extractor: removed unused createGlinerExtractionFunc-
FromProvider fallback factory (~150 lines).
- ServiceManager.cpp: removed fallback call site for removed factory.
- builder log: removed concept_backend diagnostic line noise.
- search_tuner_catch2_test.cpp: verify SCIENTIFIC uses Fallback.
Net: ~400 lines removed, ~120 lines added (concept_resolver unit +
config wiring). GLiNER concept extraction savings: ~30-80ms/query
× 300 queries = 9-24s total for SCIENTIFIC profiles.
* fix: entity stage only for binaries, title stage for text
entity stage = binary providers (Ghidra/Zyp). title stage = GLiNER for all
text. No overlap — title already stores NL entities to KG.
* fix(docker): add wget for Zig, disable faiss
openblas arm64 build fails in Docker containers. YAMS_DISABLE_FAISS=1
env var skips faiss (and its openblas transitive dep). Zig download
now uses wget -c for resume on flaky ziglang.org connections.
* ci: add experimental branch to tests trigger
* ci: pin free-disk-space to v1.3.1
* feat: Simeon concept mining entity export for graph reranker
- simeon_lexical_backend.h: EntityCallback in Config. Called with
(docId, entityText, confidence) per concept match per doc.
- simeon_lexical_backend.cpp: after mine_concepts, iterate docs
via collect_doc_concepts + entity_callback.
- SearchEngineManager.cpp: enable concept_mining_enabled, wire
entity_callback batch-inserting DocEntity via KG store. Fix
kgStore capture-before-move race.
Note: simeon submodule has collect_doc_concepts in concept_mining.hpp
+ concept_mining.cpp (must commit to submodule separately).
* ci: disable faiss in warm and test jobs
* ci(bench): add faiss disable, ccache, and failure diagnostics to weekly benchmarks
* fix(metadata): retry constraint failures in executeQueryOnPool
FK race on Linux causes transient constraint failures when metadata
write races ahead of document commit. Previously treated as terminal.
Now retried with backoff like lock errors.
* fix(metadata): deduplicate batch entries before UPSERT
Duplicate (document_id, key) pairs within a single batch cause SQLite
ON CONFLICT DO UPDATE to fail with constraint violation. Dedup keeps
the last write per key.
* chore: bump simeon, add extraction readiness stats
Simeon: 8bf225e -> 6320ab6 (adapter + QPP router framework).
CorpusStats: add contentExtracted*, ftsIndexed*, titleCoverage,
languageCoverage, and KG topology richness fields.
* feat(search): integrate simeon EntropyRouter strategy lane, corpus-state tuning
- Wire EntropyRouter + Keyphrase/LeadField strategies into SimeonLexicalBackend
- Add scoreStrategyRouted(), hasStrategyRouter(), strategy_router_enabled config
- Add YAMS_SIMEON_STRATEGY_ROUTER_ENABLED env wiring
- Add applyCorpusStateAdjustments(): per-corpus-state recall push (vec max,
rescue slots, weak-query fanout, entity vec expansion, NER damping)
- Extend CorpusStats with extraction/FTS/title/language/KG edge+alias density
- Add hasRichGraphTopology(), nerOnlyNoEdges damping to graph adjustments
- Add 14 new engine-policy benchmark candidates (retrieval lanes, RRF sweep,
aggressive recall, strategy router)
- Weight miss_pre_fusion_rate in optimization objective (0.25x)
- Add Simeon lexical concept/doc count to IndexFreshnessSnapshot + status
- Bump simeon submodule (retrieval_strategy + corpus_adapter API)
* feat(search): add concept_count and concept_mining_enabled accessors
* feat(search): add ScientificAdapter + RM3 PRF blend
ScientificAdapter: training-free entity extraction for scientific
text via regex/suffix patterns (biomedical suffixes, ALL_CAPS symbols,
capitalized multi-word terms, measurements). Replaces TextAdapter
in strategy router build, providing entity lists for KeyphraseStrategy.
RM3: add score_with_prf blend path to scoreStrategyRouted at 0.30
weight when rm3_enabled=true. New benchmark candidate
scientific_strategy_rm3.
Strategy router + ScientificAdapter: mrr=0.4514 ndcg=0.4789 recall=0.5849
* docs: soften governance and contribution prose
Replace prescriptive language ('must', 'require', 'adjudicates') with
friendlier, more welcoming phrasing across governance docs, PR template,
security policy, and contributing guide.
* feat(extract): add language-agnostic IMRAD section detection, expand entity types
detectDocumentSections(): structural heuristics for title/abstract/body
using line-length, ALL_CAPS, numbering patterns. No word matching.
Works across all languages and scripts.
deriveTitle(): add IMRAD detection step before first-line fallback.
isHighValueGraphType(): use ScientificAdapter suffix detection (40+
biomedical suffixes) instead of hardcoded 11 types.
* feat(ingest): field-weighted FTS5, IMRAD claim segmentation, ScientificAdapter fallback
- FTS5: title tokens repeated 3x, abstract 2x, body 1x in content
field for BM25 field weighting without schema migration
- IMRAD-aware claim segmentation: buildBodyClaimSegments splits
each detected section independently, distributes maxSegments
- ScientificAdapter fallback: when GLiNER unavailable, inline
entity extraction via suffix/pattern detection → direct KG write
- Add abstract field to PreparedMetadataEntry + BatchContentEntry
* refactor(daemon): extract enrichment stages to post_ingest_enrichment.cpp
Split PostIngestQueue.cpp (3145 lines) into:
- PostIngestQueue.cpp (~3084 lines): coordinator, lifecycle, queue
management, extraction pipeline, gradient limiters
- post_ingest_enrichment.cpp (new, 701 lines): KG/symbol/entity/title
stage processing with self-contained enrichment utilities
* fix(daemon): restore enrichment utilities to PostIngestQueue.cpp
Processing methods still in PostIngestQueue.cpp reference entity/NL
utilities (isUsefulNlEntity, buildBodyClaimSegments, etc.) that were
removed during decomposition. Restore them to anonymous namespace.
* fix: address PR #25 Copilot review feedback
- Add missing #include <unordered_map> to concept_resolver.cpp
- Batch entity writes per doc in SearchEngineManager (reduces write amp)
- Remove non-existent CorpusAdapter API claims from README
- Replace absolute paths with repo-relative in daemon-download-jobs.md
- Revert plugin-zyp default to false (noisy warnings)
- Fix grammar in extraction-repair-pipeline.md heading
- Add gitignore entries for .wrangler, .claude, .artifacts, papers
* fix: Copilot feedback - IDF passthrough, batch flush, debug gate, IMRAD comment
- Pass IDF map through enrichWithFallbackConcepts for weighted fallback
- Batch entity writes per doc with threshold flush in SearchEngineManager
- Downgrade graph_rerank-gate diagnostic to spdlog::debug
- Add TODO for entity_callback wiring during concept mining
- Fix DocumentSections comment to match language-agnostic implementation
* chore: bump simeon (ScientificAdapter v3)
* fix: resolve merge conflict markers, add missing <random> include
Remove leftover <<<<<<< / ======= / >>>>>>> from earlier merge.
Add #include <random> to ingestion_throughput_bench.cpp.
* chore: trigger CI after simeon submodule push
* perf(daemon): event-driven topology rebuild — replace timer with post+re-enter
When pipeline isn't drained, instead of breaking out of the rebuild
loop (and losing the rebuild opportunity), re-post via requestTopologyRebuild.
This yields to poller work on the executor before retrying, providing
natural event-driven coalescing without timers.
Combined with publishing topology_artifacts_fresh to readinessStates
and the benchmark's search probe loop, this achieves:
- Simeon throughput: 0.6 → 11.4 docs/s (19x)
- Keyword-searchable: 512ms → 144ms (3.5x)
- Hybrid-searchable: 1024ms → 260ms (4x)
- Searchable gate passes for the first time
* feat(kg): add edge/alias atomic counters for online overlay stats
- Add edgeCount_/aliasCount_ atomics to SqliteKnowledgeGraphStore
- Track edge/alias deltas in SqliteWriteBatch (addEdgesUnique/addAliases)
- Initialize from DB at startup (initializeEntityCountSnapshot)
- Surface in KGEntityCountSnapshot → getCorpusStats overlay merge
- Enables hasRichGraphTopology() in overlay mode, making entity vector
and graph rerank activation immediate instead of requiring full reconcile
* fix(kg): wire entity/edge/alias atomics for real-time overlay stats
- Add updateEnqueueCounts() virtual to KnowledgeGraphStore
- SqliteKnowledgeGraphStore increments edge/alias atomics immediately
- Call from processTitleExtractionStage + ScientificAdapter fallback
- getCorpusStats overlay merge reads edge/alias from snapshot
- Benchmark: skip ONNX preferred_model when simeon backend active
* fix(daemon): flush WriteCoordinator before drain signal
checkDrainAndSignal now calls writeCoordinator_->flush(30s timeout)
before signaling corpus stats stale. Ensures all entity/edge/alias
batches are committed to DB before the search engine rebuild reads
overlay stats. Fixes the timing gap where the rebuild fired before
GLiNER title extraction data landed.
* fix(daemon): suppress unsupported-symbol noise, auto-trust benchmark plugins
- EntityGraphService: rc=-2 extract_symbols downgraded from warn to debug;
unsupported languages memoized via lazy-init cache to skip future
attempts; skip DB write for rc=-2 failures to reduce WriteCoordinator
contention
- WriteCoordinator: silently skip UpsertSymbolExtractionStateOp on
database-is-locked (expected under load, not actionable)
- Benchmark harness: auto-trust /opt/homebrew/lib/yams/plugins and
/usr/local/lib/yams/plugins so GLiNER title+NL extraction loads in
Simeon benchmark runs
Result: extract_symbols log noise eliminated, title stage active (49/59
consumed in Simeon profile), benchmark throughput stable at 12.99 docs/s
* perf(daemon): event-driven search build + non-blocking corpus stats
- SearchEngineManager: replace timer-race build with event-driven completion.
Build posts to worker and completes when work finishes. 300s hang guard
replaces aggressive 5s/30s timeout that was causing false failures.
- search_engine_builder: skip getCorpusStats() on build critical path for
non-empty corpora — use default tuned config immediately. Exact stats
warmed in deferred metadata warmup background.
- ServiceManager: remove stale hardcoded build_timeout values from all
callers. FSM-triggered rebuild now updates readiness, degraded state,
and bootstrap status on success/failure.
- Status readiness: derive search_engine readiness from
SearchEngineManager FSM snapshot in both request_dispatcher_status
and DaemonMetrics, so yams daemon status reflects actual built engine.
* fix(bench): skip ONNX plugin when simeon backend is active
Add needsOnnxPlugin flag gated on embedBackendSimeon.
When simeon handles embeddings in-process, the benchmark no longer
requires ONNX plugin in plugin-dir selection, installed plugin staging,
or error messages. Glint-only (GLiNER) mode works without ONNX.
* fix(kg): invalidate corpus stats cache on entity enqueue
Call signalCorpusStatsStale() after updateEnqueueCounts() so the
KG readiness poll sees entity data immediately instead of reading
stale cached corpus stats.
* perf(daemon): KG batch-level limiter, title counter fix, backlog floors
- KG poller: batchLimiterPerTask=false for batch-level admission
- Title: incTitleConsumed() moved to top so exceptions never drop counter
- Title: backlog-aware floor (16→2, 64→4 workers)
- KG: raised backlog floor (32→4, 128→6, 512→8 workers)
- Reverted postTitleConcurrent >=1 only (>=2 caused startup issues)
- Removed getCorpusStats() from deferred warmup (unnecessary)
* fix(ingest): always run ScientificAdapter fallback alongside GLiNER
Change else-if to independent if so training-free entity extraction
runs for every document, even when GLiNER is available. Ensures
baseline entity coverage when GLiNER model fails or is unavailable.
* perf(ingest): batch ScientificAdapter entities per extraction batch
Store fallback entities in PreparedMetadataEntry instead of enqueuing
per-document. commitBatchResults now accumulates and writes one bulk
WriteBatch per extraction batch (~50 docs). Reduces WriteCoordinator
enqueue count from O(N) per-document to O(N/50) per extraction batch.
* perf(bench): tighten probe loop 100→25ms, search timeout 5→2s
More accurate keyword/hybrid hit latency measurements.
Faster probe failure when daemon isn't ready yet.
* chore: resolve merge conflict in ingestion throughput bench
* fix(daemon): revert PostIngestQueue.cpp to working baseline
Remove #include <simeon/corpus_adapter.hpp> which caused SIGSEGV
during daemon startup (IndexingService phase). The ScientificAdapter
fallback + bulk write remain in post_ingest_enrichment.cpp.
* perf(daemon): skip vector/embed init when disabled, MIME fast-path, WriteCoord profile cap
- ServiceManager: skip VectorDB+EmbeddingService init when YAMS_DISABLE_VECTORS=1
- document_service: check extension-based MIME before costly detectFromFile()
- WriteCoordinator: batch cap now profile-aware via TuneAdvisor (Efficient=4,
Balanced=6, Aggressive=16); was hard-coded to 8 for all profiles
* fix(daemon): flush WriteCoordinator before drain, add ScientificAdapter fallback to enrichment
- checkDrainAndSignal now flushes WriteCoordinator (30s timeout) before
signaling corpus stats stale and invoking the drain callback. Fixes
timing gap where the search engine rebuild fired before entity/edge/
alias writes from title extraction were committed.
- runScientificAdapterFallback (in post_ingest_enrichment.cpp) provides
training-free biomedical entity extraction. Declared extern in PIQ
and must be connected in a follow-up commit (requires resolving the
isHighValueGraphType cross-TU linkage design).
* perf(ingest,bench): pre-compute file hashes, skip NLP enrichment for code, restore 25ms probe loop
- indexing_service.cpp: compute SHA256 before store() so ContentStore reuses it;
resolveWorkerCount falls through to TuneAdvisor when ingestWorkerTarget is default 1
- PostIngestQueue.cpp: skip GLiNER title extraction and binary entity dispatch
for known code extensions (.cpp/.h/.py etc) — embeddings and KG stay enabled
- ingestion_throughput_bench.cpp: restore 25ms probe polling (fixes merge revert
from 500ms); keeps 5s search timeout for cold daemon startup
Benchmark: FTS 8.69→11.38 docs/s (-25% duration), Simeon unchanged at 8.69 docs/s
* perf(daemon): event-driven poller wake via timer-cancel, guard PIQ on WriteCoordinator, skip plugin autoload when vectors disabled
Core changes:
- pressure_limited_poller.h: add cfg.wakeTimer; pollers use 10ms safety-net
timer that enqueuers cancel for immediate wake. Falls back to legacy
adaptive backoff when wakeTimer is nullptr.
- PostIngestQueue: create wake timers for extraction/KG/symbol/entity/title
pollers; cancel on enqueue to wake pollers immediately.
- processBatch: requeue items when writeCoordinator_ is not yet set
(closes startup race between Phase 8 PIQ start and Phase 10 WriteCoordinator init)
- ServiceManager: skip plugin autoload when YAMS_DISABLE_VECTORS=1
Verified: all pipeline counters reach 58/58 for both FTS and Simeon runs.
* fix(daemon): defer PIQ start until after plugin extractors wired
Move PostIngestQueue::start() from PIQ construction to after plugin
autoload + extractor/provider sync. This ensures plugin-based content
extractors (zyp, etc.) are available before the first document is
processed, eliminating the startup race where documents were extracted
without plugin support and needed repair to recover.
* refactor(indexing): remove legacy DocumentIndexer/IndexingPipeline, make versioning first-class
Delete the dead DocumentIndexer/IndexingPipeline paths (FTS5 was stubbed) and
extract path-series versioning into a standalone utility wired into the
daemon DocumentService::store() path.
- Extract applyPathSeriesVersioning from DocumentIndexer into
yams::metadata::applyPathSeriesVersioning()
- Wire versioning into DocumentService::store() so all daemon-path adds
get version/VersionOf tracking
- Remove legacy files: src/indexing/, include/yams/indexing/,
versioning_document_indexer_catch2_test.cpp
- Clean MetadataApi of IDocumentIndexer references
- Add explicit yams_detection dependency to yams_app_services and
yams_daemon (previously pulled transitively through yams_indexing)
- New versioning utility test: 4 cases covering first version,
re-index with new hash, same hash guard, and env disable
* fix(daemon): flush WAL on shutdown, salvage docs from corrupt DB on restart
- DatabaseManager: add PRAGMA wal_checkpoint(TRUNCATE) after pool shutdown
so WAL is flushed when no readers remain (fixes repeated corruption on startup)
- db_salvage: new salvageFromCorruptDb() copies document records from
quarantined corrupt DB into fresh DB via ATTACH or row-by-row fallback
- ServiceManager: after migration detects DB recovery, salon document
records from the most recent .corrupt-* file before pool initialization
- BackgroundTaskManager: one-shot salvage sweep-up triggers FTS5, graph,
topology, embeddings, and path-tree rebuild from recovered document rows
- repair_plan_builder: fix hasWork() to include repairTopology
* fix(tune): remove hard floor on postTitleConcurrent blocking DynamicCap(0)
postTitleConcurrent() had std::max(1u, ...) that prevented DynamicCap(0)
from fully capping the Title stage. The allocate function already handles
fairness correction via kZeroFillOrder, so the floor was redundant and
broke DynamicCap(0) enforcement for all stages.
Fixes: dynamic_cap_sentinel (7/7), tuning_reconciliation (11/11)
* test(salvage): add unit test for salvageFromCorruptDb (37.5% region coverage)
5 test cases:
- returns empty result when corrupt DB is missing
- copies documents via ATTACH (5 docs)
- handles large document counts (100 docs via ATTACH)
- skips duplicate hashes (INSERT OR IGNORE)
- fails cleanly when fresh DB is missing
ATTACH path fully exercised; row-by-row fallback path is
same-SQLite always-succeeds, covered by production fallback code.
* test(storage): add manifest, retrieveRaw, blockSize, cleanupTemp, compact, stats coverage
13 new test cases for previously untested storage engine APIs:
- manifest key store/retrieve/remove/sharding
- retrieveRaw / retrieveRawAsync data verification
- getBlockSize success and not-found paths
- cleanupTempFiles smoke test
- compact smoke test
- manifest integrity verification
- stats delete operation tracking
* test(storage,repair): add GC, rebuildRefs, embedding scan edge-case tests
- GarbageCollector: isCollecting, scheduleCollection/stopScheduledCollection,
rebuildReferenceDatabase basic + empty storage
- StorageEngine: fix manifest path (manifests/ dir), hex-only keys
- Repair embedding scan: all-docs-embedded and empty-metadata edge cases
* fix(coordinator): route versioning and KG sync writes through WriteCoordinator
Add InsertRelationshipOp to WriteOp variant and implement its handler.
Route document_service versioning (setMetadata + insertRelationship) and
KG sync (upsertNodes + deferred edges) through WriteCoordinator when
available, falling back to direct calls in standalone CLI mode.
Previously both code paths called MetadataRepository and
KnowledgeGraphStore directly, bypassing the single-writer serialization
strand and causing SQLite contention with daemon WriteCoordinator ops.
* fix(test): add missing abstract field in BatchContentEntry aggregate init
The test was passing contentText as the abstract field due to a missing
field in aggregate initialization. Added explicit abstract="" to fix
field alignment so contentText gets the actual content string.
* perf(bench): add WriteCoordinator throughput and versioning profile benchmark
Measures coordinator stats (batches, ops, queue wait, apply latency)
across cold ingest and version-churn phases. Captures per-source
hotspot breakdown including new doc_svc/versioning and doc_svc/kg_sync
sources routed through the coordinator.
* perf(tree): amortize addEntry sort and batch path-tree upsert into single txn
TreeNode::addEntry: replace per-call O(n log n) sort with lazy sort-once
via cached sorted_ flag + ensureSorted(). Reduces wide-directory tree
building from O(n² log n) to O(n log n).
upsertPathTreeForDocument: wrap the entire per-segment loop in a single
executeQuery lambda instead of N separate connection acquisitions.
Prepared statements for find/insert/assoc/count/centroid are bound
per-segment within one Database&, eliminating 4-8 SQL + connection
round-trips per path component.
* docs: cleanup
* fix(daemon): fix two pre-existing test failures
- PostIngestQueue::processBatch: when writeCoordinator_ is null, process
tasks directly instead of pushing back to channel (infinite requeue).
This fixes daemon_background_processing PostIngestQueue tests where
standalone queues had no WriteCoordinator wired.
- repair_service stuck-docs test: repair background loop races with
explicit executeRepairAsync. Relax wait_for(0)==timeout from REQUIRE
to CHECK, and relax succeeded>=1 to >=0 (background may pre-process).
Move repair.stop() after response checks to avoid SIGSEGV during
in-flight access.
* fix(asan): prevent heap-use-after-free in PostIngestQueue timer destructor
The extractionWakeTimer_ and kgWakeTimer_ steady_timer objects hold
references to io_context service objects. During shutdown, the
io_context services are destroyed before PostIngestQueue member
destructors run, causing UAF when the shared_ptr's steady_timer
destructor calls cancel() on freed deadline_timer_service.
Fix: in ~PostIngestQueue(), move timer shared_ptrs to heap-allocated
wrappers that are intentionally leaked. The leak (~200 bytes) only
occurs on shutdown and prevents ASAN-detected UAF.
