Graph explore matched candidates across the whole knowledge graph by
label, then filtered by scope. For a bare basename with many foreign
matches the global ORDER BY label LIMIT filled every slot before scope
filtering, so the correct in-scope file never appeared. For a single
absolute path, logical, historical and blob representations of the same
file consumed the symbol budget and the reported files.
Seed an explicit single-term file-like target through scoped direct-key
lookup instead of relying on the saturated global pool, and rank the
remaining candidates by query coverage. Collapse whole-file hydration
representatives to one entry per path while keeping every contributing
node identity for relationship collection, so distinct symbols, text
segments and explicit source spans are still emitted. Raw lookup is
unchanged and still returns all nodes.
Truncation accounting now covers clipped snippets and omitted unreadable
sources. Explore hints keep an external target and add --global when the
target resolves outside the current directory; local hints stay scoped.
Tests cover scoped lookup under a saturated foreign label pool, file and
version budget diversity, direct-key seeding, relationship retention
across duplicate file representations, segment provenance, the
relationship cap, disabled relation and zero-symbol budgets, and
external hint scope.
Signed-off-by: trvon <git@trevon.dev>
* test(graph): cover --topology-clusters --scope-cwd outside src/include
Follow-up to #280. --topology-clusters --scope-cwd still built its
scope from <cwd>/src and <cwd>/include, so a corpus laid out any other
way had no scoped members:
- The scope path set must hold every stored path under the cwd, also
when the cwd is reached through a symlink, and not a sibling that
shares the prefix.
- GraphTopologySupport must build the set from its own metadata repo.
The existing cluster-scope case built its path set by hand from the
old src/include contract. It now builds the set from /repo, so
/repo/tests/ is in scope and a document outside /repo is not.
Signed-off-by: trvon <me@trevon.dev>
* fix(graph): scope --topology-clusters --scope-cwd to the whole cwd
Follow-up to #280. Topology views built their --scope-cwd path set from
<cwd>/src and <cwd>/include only, a leftover from the code-symbol graph
removed in v0.20. Corpora laid out any other way reported no scoped
members.
Build the set from the same roots as the --list-type ranges: the cwd,
lexical and symlink-resolved. Keep only paths really under a root, since
the prefix query matches with LIKE. The topology view no longer prunes
build/, packages and IDE paths, so it matches --list-type.
GraphTopologySupport now builds the set from its own metadata repo
instead of the CLI app context. Remove buildGraphCodeScopePathSet and
buildGraphCurrentScopePathSet, which have no other callers, and use one
"Scoped to paths under the current directory" note for both views.
Signed-off-by: trvon <me@trevon.dev>
* test(cli): cover graph --name on a document with a path:file: node
Follow-up to #280. yams graph --name <path> tried path:file:<path>
node keys before the document lookup. v0.20 ingestion writes
path:logical: and path:<snapshot>: keys, so the probe misses on a
fresh corpus; after `yams doctor repair --graph` (or NL entity
extraction) the key exists, and --name printed a raw traversal of the
file node instead of the document's related documents.
Smoke cases through the in-process CLI:
- --name on a file with a path:file: node returns its hash and its
semantic neighbours (red).
- A relative --name resolves under the cwd even though a newer copy
with the same relative path exists in another checkout.
- A bare file name still resolves by name.
The portability allowlist entry for this file moves with its getenv
line.
Signed-off-by: trvon <me@trevon.dev>
* fix(cli): resolve graph --name through the document lookup only
Follow-up to #280. yams graph --name first traversed path:file:<path>
node keys. v0.20 ingestion writes path:logical:<path> and
path:<snapshot>:<path>, which only chain to blob versions; semantic
neighbours hang off doc:<hash>. On a fresh corpus the probe always
missed. After `yams doctor repair --graph` or NL entity extraction it
hit and printed a raw file-node traversal instead of the related
documents.
Drop the probe and go straight to the document lookup, which starts at
doc:<hash> since #280. Resolving to path:logical: instead would show
the version chain, not related documents; --node-key still traverses
any node.
Send --name as the path ingestion stores: relative to the client cwd,
lexically normalized, symlinks resolved. The daemon resolved relative
names against its own cwd and fell back to a suffix match, which picks
the newest copy across checkouts. Fall back to the name as given when
it does not resolve, so bare file names and suffixes still work.
build_graph_file_node_candidates had no other callers; its tests are
replaced by tests for buildGraphDocumentNameCandidates.
Signed-off-by: trvon <me@trevon.dev>
* test(graph): cover --limit on the document graph lookup
Follow-up to #280. yams graph <hash> and --name ignored --limit: the
daemon capped the graph query at 100 nodes and the same-directory
fallback at 20 documents.
Smoke cases through the in-process CLI:
- --limit 1 returns one related document by name and by hash, and the
first of the uncapped list.
- --limit 1 caps the same-directory fallback for a document without
graph edges.
- Without --limit the related lists are unchanged.
Signed-off-by: trvon <me@trevon.dev>
* fix(graph): pass --limit through the document graph lookup
Follow-up to #280. yams graph <hash> and --name sent --depth but not
--limit; DocumentService fixed the graph query at 100 nodes and the
same-directory fallback at 20 documents.
Add GetRequest.graph_limit (proto field 27) and
RetrieveDocumentRequest::graphLimit, and pass them from the CLI through
the dispatcher. A limit caps the related list, graph neighbours, path
history and the same-directory fallback alike. The graph query never
asks for fewer than 100 nodes, since path and blob nodes count toward
that limit.
The CLI sends a limit only when --limit is given; 0 keeps the old caps,
so default output is unchanged. The binary GetRequest layout appends
the field and still reads payloads without it.
Unit tests cover the proto round trip, the dispatcher mapping and the
DocumentService caps.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* test(graph): cover document lookup and --scope-cwd listing (#280)
Red tests for the two graph CLI bugs in #280:
- GetResponse graph fields and file name must survive the proto wire.
- DocumentService graph lookup by hash and by name must return the
same documents as traversing the doc:<hash> node.
- The document graph JSON must name the document when only name is set.
- KG path-range scoping must match document nodes by label and
snapshot path nodes by $.path.
- listByType --scope-cwd must keep document and path nodes under the
client cwd (including via a symlinked cwd) outside src/ and include/.
The existing code-roots dispatcher case now places its out-of-scope
file outside the scope root, since the scope is the whole cwd.
Signed-off-by: trvon <me@trevon.dev>
* fix(graph): fill document lookup and scope --scope-cwd to the cwd (#280)
yams graph <hash> and --name returned graphEnabled=false with no
related documents while --node-key doc:<hash> listed neighbours:
- The GetResponse proto binding dropped graphEnabled, related and
fileName, so socket clients never saw graph data.
- DocumentService started traversal at blob:<hash>, which has no
outgoing edges, and filtered out semantic_neighbor. Start at the
doc:<hash> node and allow semantic_neighbor.
- GraphQueryService did not hydrate documentHash for doc: nodes, so
reached documents were skipped.
- The presenter read only fileName for "document"; fall back to name.
--list-type <t> --scope-cwd returned nothing:
- The daemon scoped to <cwd>/src and <cwd>/include only. Scope to the
whole cwd, lexical and symlink-resolved.
- The KG range predicate ignored document labels and $.path on
snapshot path nodes. Match both.
Signed-off-by: trvon <me@trevon.dev>
* docs(skills): correct graph document lookup examples
--format dot is only rendered for node traversal, so show it with
--node-key doc:<hash>. Describe --scope-cwd as cwd-scoped.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* chore(warnings): default-initialize aggregate members left out of brace-init
GCC -Wmissing-field-initializers fired about 1300 times where tests and
src build structs with a short positional brace list. Give the omitted
members an empty default member initializer. Value-initialization from
{} is what aggregate init already did for them, so behavior is
unchanged.
Signed-off-by: trvon <me@trevon.dev>
* chore(warnings): remove or annotate unused parameters, functions and variables
- init_command, s3_signer test, request_handler_lifetime test: comment out
the unused parameter name.
- video_content_handler: path is only read under YAMS_HAVE_FFPROBE.
- vector_memory_scaling_bench: main() takes no arguments.
- daemon_status_render: delete unused neutralText helper.
- DaemonMetrics: mallocStackLoggingNoCompactEnabled is only called in the
__APPLE__ block, so define it there.
- SocketServer: einval_streak only matters in the __APPLE__ EINVAL path.
- onnx_plugin_harness test, vector_backend_engine_compare bench,
work_coordinator test: mark platform-conditional or busy-loop
variables [[maybe_unused]].
Signed-off-by: trvon <git@trevon.dev>
* chore(warnings): fix sign-compare, range-loop, nodiscard and dangling-ref in tests
- search_admission_controller: count started workers in std::uint32_t so
the comparison with the uint32 cap is same-signed.
- p2p_manager: iterate the invalid-host list by const reference.
- integrity_verifier: discard the nodiscard results the tests do not
inspect with static_cast<void>.
- post_ingest_queue: findNode/findEdge take std::string_view so no
temporary std::string is created for the call (GCC
-Wdangling-reference false positive on the returned reference).
- topology_ablation_bench: the doc comment ended a line with a backslash,
which continues the comment (-Wcomment); show the env export on its own
line.
Signed-off-by: trvon <git@trevon.dev>
* chore(warnings): drop redundant std::move of a const captured json
The coroutine lambda is not mutable, so the captured optional<json> is
const and std::move(*progressToken) already selected the copy assignment.
Drop the std::move so the code states what actually happens.
Signed-off-by: trvon <git@trevon.dev>
* chore(warnings): mark __int128 use in db_integrity_stamp as an extension
-Wpedantic flags __int128. Use a __extension__ typedef, the GCC/Clang
idiom for an intentional extension, instead of the bare keyword.
Signed-off-by: trvon <git@trevon.dev>
* chore(warnings): remove always-true unsigned >= 0 comparisons
GCC -Wtype-limits flagged 51 test assertions of the form
CHECK(unsignedValue >= 0) that can never fail, plus a dead
`totalCount.value() < 0` clause in the graph listByType handler (the
count is std::size_t). In the tests keep the evaluation as a
static_cast<void> so the accessors are still exercised; in the handler
drop the dead clause and keep the range check.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
Signed-off-by: trvon <git@trevon.dev>
v0.20 stopped producing code-symbol nodes and calls/references/
inherits/implements edges, and migration 40 deleted the existing ones.
GraphContextService::impact() and affectedTests() had already been
reduced to returning a "code-symbol graph was removed" warning, so
`yams graph --impact`, `--affected-tests` and `--test-pattern` (and the
MCP graph actions `impact` and `affected_tests`) could only ever print
that warning.
Remove the dead surface:
- CLI: the three flags, their execute/render helpers, and the --impact
mention in the --global help text.
- MCP: the two actions, their schema entries and the changed_files /
test_pattern request fields. Unknown graph actions now fail with
InvalidArgument instead of silently running a default query.
- Service: impact()/affectedTests() and their request/response structs.
The GraphImpact/GraphAffectedTests IPC messages stay for wire
compatibility. The dispatcher now answers them directly with the same
removal warning, without touching the metadata repository.
Kept: --lookup (with --at-file) and --trace/--to. Both resolve graph
node labels and aliases and walk edges of any relation, so they still
work on document, path, version and entity graphs.
Tests: the service-level impact/affected-tests case moves to the
dispatcher graph suite; the sandbox smoke test now expects --impact to
be rejected. docs/prompts/PROMPT-eng-codex.md points related-test and
blast-radius questions at `yams grep`.
Signed-off-by: trvon <me@trevon.dev>
ClientConfig::acceptCompressed was written by RetrievalService's config
mapping and compared in the CLI client-pool equality operator, but no
DaemonClient or transport code ever read it, so it could not change
behavior. Compression is negotiated per request through
GetRequest::acceptCompressed, which RetrievalOptions::acceptCompressed
still feeds via makeGetRequest.
Drop the field, the mapping, the equality term (configs that differed
only in this flag now share a pooled client, which is what their
behavior already was), and the mapping-test assertion. The per-request
flag and its tests are unchanged.
Signed-off-by: trvon <me@trevon.dev>
A clean `yams daemon restart` never published the clean-shutdown
integrity stamp, so every start paid for a full PRAGMA quick_check
(13-27 min on a 93 GB database). Request handlers offloaded to
WorkCoordinator threads (list, grep, get, search) kept running through
Phase 5: nothing interrupted a long SQLite statement or a long result
loop, both 5 s and 30 s joins expired, the workers were abandoned, and
the stamp was disabled.
Shutdown now tells in-flight work to stop before joining:
- ConnectionPool::interruptActiveConnections() calls sqlite3_interrupt
on every leased connection under the pool mutex, which keeps each
lease open while it is interrupted. DatabaseManager exposes it for
both pools. Phase 4 interrupts once, and Phase 5 re-interrupts on each
join wait slice through a new joinWithTimeout hook, because SQLite
drops an interrupt that lands between two statements.
- ServiceManager owns a shutdown cancellation flag, set at Phase 4
before the interrupt, and publishes it as AppContext::cancellationSignal.
DocumentService::list and GrepService::grep check it between query
and hydration steps and between document batches, and return
OperationCancelled; SearchService checks it on entry and forwards it
as SearchExecutionContext::hostCancellationSignal, which the engine's
existing cancellation checks and the fanout collector now honor.
- The concept-extraction wait no longer blocks without bound when
componentTimeout is 0, and a canceled search stops waiting for the
query embedding / concept tasks. Those tasks now own copies of their
inputs instead of capturing the caller's stack, so abandoning them is
safe.
Interruption stays scoped to shutdown: the flag is only set in Phase 4
and cleared on initialize, and interrupting an idle lease does not fail
its next statement.
Also erase a connection from the leased set when its rollback throws;
it was left behind as a dangling pointer, which the interrupt walk
would have dereferenced.
Signed-off-by: trvon <me@trevon.dev>
parseQueryQualifiers parsed lines:, pages:, section: and selector: into
an ExtractScope "for downstream snippet shaping", and SearchService then
used only its name/ext/mime hints: the scope itself was ignored, so
`yams search "foo lines:1-20"` silently searched for "foo" and returned
ordinary snippets.
- lines:<range> now replaces each result's snippet with those lines of
its stored content (1-based, e.g. "1-3,10"), through the same
TextBasicHandler `get` uses. It runs after snippet hydration, so
nothing overwrites it, and only when the qualifier is present.
- A result with no line-range handler (binary formats such as PDF),
content over 1 MiB, or unreadable content keeps its snippet and is
counted, never presented as shaped.
- pages:, section: and selector: have no search-time handler; they are
now reported rather than silently dropped.
- The outcome ("lines:1-20 applied to 7 of 8 results (1 without
line-range text, ...)" or "pages:1-2 is not applied to search
results") goes into searchStats["extract_scope"] and queryInfo, which
the MCP response already carries.
The logic is a header-only seam, applyExtractScope
(<yams/app/services/extract_scope.h>), tested directly for shaping,
unsupported formats, the read cap, an invalid range, pages:, and no
qualifier; plus an end-to-end SearchService test that fails before this
change: every hit for "programming lines:1-1" carries exactly its
document's first line.
Cost: a lines: query reads each result's content once (bounded by the
result limit and the 1 MiB cap); queries without the qualifier are
unchanged.
The portability allowlist entry for search_service.cpp's reviewed
getenv moves from line 509 to 510 with the new include.
Found by pipe's experimental C++ front end: ExtractScopeType values were
produced by the parser but never examined anywhere.
SymbolEnricher boosted results by looking up code-symbol nodes that no
longer exist since v0.20, so it ran KG queries for the top results and
never boosted anything. Remove it, the YAMS_SYMBOL_WEIGHT variable, the
symbol_rank_* search stats, and the symbolRank option on the service,
retrieval, MCP and CLI request types. The IPC field stays in the wire
format but is ignored, and --symbol-rank/--no-symbol-rank remain
accepted as hidden no-ops so existing scripts keep working.
Graph explore looked up entry points in symbol_metadata, which no longer
exists. Resolve them from node labels, aliases, and ingest path nodes
instead, gather a wider candidate pool, and rank it by query-term
coverage per file before applying the symbol budget so broad early
terms cannot crowd out the file that answers the query.
Impact and affected-test analysis walked code-symbol edges that are no
longer produced; they now return a warning saying the symbol graph was
removed in v0.20 instead of silently empty results.
- Remove enable_symbol_extraction option and tree-sitter requirement from conanfile.py.
- Remove YAMS_DISABLE_SYMBOL_EXTRACTION toggles from setup.ps1, setup.sh, and ubuntu.Dockerfile.
- Add v39_metadata_db_template helper to MetadataDbTemplate for legacy symbol tests.
- Update GraphComponent, DeleteCascade, GraphContextService, and KGStore test
fixtures to run symbol-specific test cases against schema v39.
Signed-off-by: trvon <me@trevon.dev>
* 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>
* perf(search): preview-based rerank text and compiled path globs
Cross-rerank built each window entry's text with a full getContent()
read, then kept only the first rerankSnippetMaxChars characters. The
window now hydrates with one batchGetContentPreview() call bounded to
that many characters; buildCrossRerankText takes the preview instead of
the repository. batchGetContentPreview is virtual so a test can count
it: three window results cost one preview batch and zero full reads.
Path filtering compiled a std::regex from the glob on every call, and
the call sits inside per-document loops in pathSearch, the hash-prefix
search, and metadata filtering. GlobMatcher (src/app/services) holds
the compiled form; wildcardMatch() reuses it through a small
per-thread cache. The glob semantics are unchanged and now pinned by a
test: '*' stays within one path segment, '**' crosses, '?' is one
character, regex metacharacters are literal. yams::common::wildcard_match
was considered and rejected because its '*' crosses separators.
portability_allowlist.txt: two search_service.cpp anchors reflowed.
Signed-off-by: trvon <me@trevon.dev>
* perf(search): parse edge anchor properties once, lower the path query once
Graph expansion parsed every visited edge's JSON properties with
nlohmann::json::parse to read at most two strings, region and scope,
in three places (relation weighting, seed anchoring, and neighbour
anchoring). Properties strings repeat heavily across edges and most
carry no anchor at all. edgeAnchorHints() now returns immediately when
the text cannot contain either key and otherwise parses each distinct
string once per thread through a small bounded cache. A process-wide
parse counter lets the test pin it: one hundred lookups of the same
anchored string cost one parse, and un-anchored or malformed strings
cost none.
computePathMatchScore lowercased and trimmed the query for every
candidate document; pathSearch now does that once and passes the
lowered query down. The existing path-search tests cover the scoring.
portability_allowlist.txt: two search_service.cpp anchors reflowed.
edgeAnchorHints returns its two short strings by value: the per-thread memo
clears itself at 1024 entries, so a reference into it could dangle across
calls even though today's three callers consume the result immediately.
Signed-off-by: trvon <me@trevon.dev>
* fix(search): preserve hydration failure semantics
Stop reranking before scorer calls or score changes when previews fail.
Commit anchor hints atomically and recognize escaped JSON keys.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* perf(search): load tag filters once per request, not once per document
pathSearch and searchByHashPrefix filtered candidates through
metadataHasTags(), which for every document called getAllMetadata()
(four retries with backoff on failure), concatenated every metadata
key and value into a string, and logged that string at info level.
A path search over a few thousand documents was a few thousand
metadata round trips and a few thousand info lines.
Both paths now load tags for the whole candidate set with one
batchGetDocumentTags() call (the API GraphComponent already used) and
filter with a pure matcher. The legacy fallback that also accepted a
metadata row with key "tag" is gone: nothing writes that form and the
repository's own tag APIs never honoured it, so search and repository
now agree on what a tag is.
A counting repository subclass pins the shape: one batch call and zero
getAllMetadata calls for both the path and the hash-prefix routes.
portability_allowlist.txt: two search_service.cpp anchors reflowed.
Correction to the claim above that nothing writes the legacy `key = "tag"`
form: the repair downloads pass did (tag values "downloaded", "host:<h>",
"scheme:<s>"), and the search fallback was its only reader. That writer now
uses the same `tag:<name>` keys as every other tag writer, so `--tags
downloaded` keeps matching documents the repair pass tagged. And
batchGetDocumentTags chunks its IN list (500 ids), since pathSearch feeds it
an unbounded candidate set; an oversized list used to fail the statement
and, with this change, would have emptied the result instead of degrading
per document.
Signed-off-by: trvon <me@trevon.dev>
* perf(search): hydrate topology routing candidates in batches
The routing session called getDocumentByHash once per hash in three
places on the product routing path: ranked-candidate admission, cluster
expansion, and the graph-neighbor diagnostic trace (memoized, but still
one statement per distinct hash across four stages). Each now issues
one batchGetDocumentsByHash for its whole set, the same API the
topology input extractor already used, and the docLookupMicros timing
covers the batch. Cluster expansion applies the maxDocs cut before
hydrating so no document is fetched only to be discarded.
A session-level test with one seed and eight graph neighbours under a
counting repository fails on the previous code (17 single lookups, no
batch) and passes now (0 single lookups). The full topology suite is
unchanged.
portability_allowlist.txt: one topology test anchor reflowed.
Signed-off-by: trvon <me@trevon.dev>
* fix(search): bound hydration and preserve errors
Retain legacy tags and honor per-connection SQLite bind limits.
Keep hash chunks in one read snapshot and release it on failure.
Failed lookups are not missing documents or successful empty searches.
Reject partial route admission and preserve tagged path errors.
Signed-off-by: trvon <me@trevon.dev>
---------
Signed-off-by: trvon <me@trevon.dev>
* fix(memory-sync): keep replication responsive
Skip poisoned blobs without wedging backfill and publish immutable status snapshots so daemon IPC does not block on an active reconciliation cycle.
Reconstructed from ff62d3f8, 8e232721, and e60f513d.
Signed-off-by: trvon <git@trevon.dev>
* feat(p2p): add authenticated direct transport
Require TLS 1.3 mutual identity and bind the authenticated certificate, node, corpus, and epoch before replication state is exchanged.
Reconstructed from 96f9db88 and c46de77b.
Signed-off-by: trvon <git@trevon.dev>
* feat(p2p): exchange causal deltas
Persist peer pins and causal resume state before visibility so reconnects continue bounded authenticated replication without becoming remote query proxies.
Reconstructed from 1b8be146 and 41883338.
Signed-off-by: trvon <git@trevon.dev>
* feat(p2p): integrate direct sync services
Wire listener, reconnect, IPC, CLI, peer persistence, and daemon lifecycle around the authenticated direct transport.
Reconstructed from a19aaa44.
Signed-off-by: trvon <git@trevon.dev>
* fix(p2p): apply replicated document state
Index authenticated remote winners, propagate document tombstones, and keep service/test wiring complete across daemon paths.
Reconstructed from 4ca660c6, 443253f1, 3e9db24d, and 4b2ddcc5.
Signed-off-by: trvon <git@trevon.dev>
* test(p2p): register direct sync gates
Replace the superseded internal contract with operator-facing direct-sync guidance and register daemon integration coverage in the standard test layout.
Reconstructed from 360b9115 and 89416ccb.
Signed-off-by: trvon <git@trevon.dev>
* fix(p2p): require bounded peer enrollment
Bound aggregate sessions and worker lifetimes, create owner-only identity keys atomically, and reject unknown inbound peers until operators pin their mTLS identity.
Reconstructed from f91be528, 79de8e48, 4fb1e4b8, dc30a6c0, and b329edd3.
Signed-off-by: trvon <git@trevon.dev>
* fix(p2p): persist quarantine and deletes
Persist full-history writer commitments before invalidating forked state, and order local deletion through a durable authenticated outbox so tombstones survive crashes and reconnects.
Reconstructed from 74ce01e0 and 19888604.
Signed-off-by: trvon <git@trevon.dev>
* feat(p2p): add authenticated cold bootstrap
Install bounded zero-state snapshots only from previously operator-pinned peers, bind them to exact frontiers and full-history commitments, and recover staged journals before replication can resume.
Reconstructed from 8a9f5acf.
Signed-off-by: trvon <git@trevon.dev>
---------
Signed-off-by: trvon <git@trevon.dev>
Xcode 16.4's Apple libc++ lacks std::jthread; the deadline test used
it directly, breaking the macos-arm64 build. Use the repo's existing
yams::compat::jthread shim (native alias when available, std::thread
fallback otherwise).
* 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
Honor root-anchored and slash-qualified ignore patterns during live fallback. Center hydrated snippets on query matches and preserve symbol ranking through the daemon boundary.
Rank natural-language graph matches by multi-term file coverage, repair stale in-bounds snippet locations, and replace affected-test label scans with bounded batch traversal. Correct the YAMS-first prompt to route relationship questions through the matching graph operation.
* fix(graph): handle qualified C++ symbols
Signed-off-by: trvon <me@trevon.dev>
* refactor(vector)!: remove dead transition APIs
Split Simeon vector and retrieval linkage so consumers inherit only the runtime surface they use.
BREAKING CHANGE: remove unused async/model/config helpers and the undefined vector-backend factory from public headers.
Signed-off-by: trvon <me@trevon.dev>
* fix(vector): harden PQ snapshot lifecycle
Validate and atomically install persisted generations, revalidate after races, and fall back to exact search when a snapshot is stale. Add the exact-scan reference lane and distinguish observed work counters from unavailable backend metrics.
Signed-off-by: trvon <me@trevon.dev>
* feat(topology): expose route coordinates
Persist chart distortion and local-dimension evidence, retain pre-scalarization route axes, and emit detailed trace rows without treating unavailable vector work as zero.
Signed-off-by: trvon <me@trevon.dev>
* feat(xplan): add vector decision gates
Track binary and corpus identity, preserve missing-work semantics, and add repeated PQ routing, crossover, and rerank plans with quality and cost summaries.
Signed-off-by: trvon <me@trevon.dev>
* feat(topology): formalize coordinate routing
Separate chart geometry from route-risk admission and prove candidate-stage recall and strict-focus boundaries. Record the measured atlas limitations and literature basis for the next construction experiment.
Signed-off-by: trvon <me@trevon.dev>
* fix(search): serialize SymSpell readers
SQLite-backed lookups reuse mutable prepared statements, so shared-reader locking is unsafe. Advance the owned SymSpell revision for batched delete insertion and cover concurrent root lookups under TSAN.
Signed-off-by: trvon <me@trevon.dev>
* fix(vector): make mutations atomic
Preserve stored vectors on replacement and commit failures, reject cross-thread writes during explicit transactions, and restore exact reranking for quantized-primary PQ rows.
* fix(search)!: surface SymSpell write errors
Propagate persistent dictionary failures through metadata ingestion, roll back failed batches, and make clear remove stored terms.
BREAKING CHANGE: SymSpellSearch mutations now return Result values.
* feat(topology): formalize candidate expansion
* feat(vector): add coordinate-aware embeddings
* feat(topology): preserve protected relation cover
* feat(search): add graph candidate rescue
* feat(daemon): expose retrieval hydration telemetry
* feat(xplan): add rescue and hydration gates
* refactor(content): dedupe media handlers
Reuse shared graph presenter helpers and centralize repeated audio/video/archive buffer processing, validation, lifecycle, and stats helper logic.
* feat(lifecycle): prune stale corpus data
Keep cleanup preview-first while retention stays opt-in and long prune work no longer holds IPC responses open.
* feat(search): add topology candidate rescue
Preserve high-value routed candidates across vector backends while keeping exact rerank diagnostics explicit.
* feat(search): expose evidence paths
* docs: define mobile host contract
* formal: model bounded candidate rescue
* fix(prune): inspect extensionless signatures
* fix(prune): tolerate stale extensions
---------
Signed-off-by: trvon <me@trevon.dev>
* fix(daemon): harden model state ownership
Keep ModelPoolConfig single-defined and serialize telemetry snapshots to avoid ODR drift and torn concurrent reads.
* refactor(daemon): consolidate ingest pollers
Require the wake-timer contract so every post-ingest stage shares one event-driven poller configuration.
* refactor(daemon): unify repair execution
Share admission, operation ordering, cancellation, progress, and result aggregation between synchronous and asynchronous repair paths.
* refactor(daemon): unify runtime tuning
Resolve startup and reload settings through one typed path so parsing, precedence, and range validation cannot drift.
* refactor(daemon)!: remove dead IPC surfaces
Delete unreferenced framing, cancellation, and compatibility paths while keeping the active streaming protocol intact.
BREAKING CHANGE: callers using connectAsync or legacy MessageFramer and FrameReader helpers must migrate to connect, frame_message_into, feed, and get_frame.
* refactor(daemon): hide test hooks
Preserve test-library linkage without exposing daemon-only probes through production headers or external symbols.
* fix(daemon): avoid replaying successful adds
A fresh-connection transport retry reuses the response handler. Clear its stale EOF error when the retry returns a valid add response so the outer retry loop does not enqueue the document again.
* bench(ingest): enforce lossless pipeline runs
Separate admission, storage, drain, enrichment, and searchability timing. Decision-grade plans now reject drops, duplicate processing, incomplete pipelines, and experiment identity drift.
* bench(search): expose cold seed ingest timings
Pair generalized-memory quality arms with admission, storage, drain, searchability, and enrichment timing from their shared cold seed. Keep the observation distinct from repeated throughput measurements.
* perf(ingest): batch deferred content indexing
Directory ingestion already schedules content work through post-ingest. Avoid duplicate inline indexing and coalesce normal-priority trickles within a bounded window.
* feat(metadata): expose insert writer metrics
Separate queue, batch-apply, and transaction time so ingestion runs can attribute connection pressure without changing write semantics.
* fix(daemon): retry transient refused connects
The daemon socket can be bound before its listener is ready during startup. Reuse the existing bounded retry budget for that refusal window.
* bench(ingest): attribute submission path costs
Decision-grade runs need stable coalescing identity and separate queue, apply, transaction, and estimated connection-wait costs.
* perf(ingest): batch durable document storage
Commit chunks, manifests, references, and metadata in bounded batches while preserving publication only after durable reference success.
* perf(ingest): coalesce bulk post-processing
Use a 16-item bulk cap while keeping latency-sensitive daemon ingestion on the existing four-item priority quota.
* bench(ingest): record post-ingest batch size
Include the effective cap in metrics and experiment identity so runs with different batching policies cannot be compared as one system.
* perf(ingest): batch queued storage waves
Preserve single-document fallback semantics and execute inline when the coordinator has one worker to avoid self-deadlock.
* perf(ingest): route bulk enrichment batches
Keep quota-sized interactive groups on the RPC lane while sending larger lossless groups through bounded coalescing.
* test(daemon): initialize task fixtures
* perf(ingest): batch post-ingest dispatch
* perf(ingest): widen directory storage waves
Borrow from a full wave when one document would otherwise fall through to single-document storage.
* perf(storage): bound batch writer fanout
Reuse a fixed worker set so batch size no longer creates one thread and payload copy per object.
* perf(ingest): align storage batch drains
Dispatch one configured batch through storage so intermediate waves do not fragment downstream metadata work.
* fix(ingest): commit metadata state atomically
Fold first-version, extracted-title, and embedding-completion state
into existing transactions.
Read committed extraction state so duplicate-content tasks cannot
double-count corpus counters.
* bench(ingest): measure production submission
Drive pipelined files through DocumentIngestionService.
Export dispatch, fingerprint, and enqueue costs through xplan.
* fix(xplan): preserve native failures
Report child signals and bounded stderr before readiness checks so
assertions are not masked as missing traces.
* fix(daemon): preserve embedding success hashes
* fix(daemon): serialize pooled socket shutdown
* fix(daemon): harden batch publication shutdown
* fix(storage): use compat jthread shim
* fix(daemon): avoid poller template shadowing
* fix(search): keep vector pipeline test enabled
* fix: harden shutdown and fallback paths
Demote expected shutdown SQL interruptions, ignore readonly FTS integrity noise, avoid stopped-executor socket hangs, and preserve metadata writer fallback outcomes.
* 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
* perf(daemon): coalesce metadata writes
* refactor(metadata): split repository ops
* fix(metadata): harden repository invariants
* feat: test coverage and continued refactor work in metadata code
* fix(graph): handle path-like explore queries
- prefer file path symbol lookup for graph explore\n- sanitize alias FTS queries before MATCH
* fix(daemon): quiesce shutdown background work
- Interrupt pending DB acquires before worker shutdown
- Wait for tracked background coroutines and timers to drain
* fix(daemon): cancel repair work on shutdown
Blocked embed and post-ingest queues could keep salvage and\nstuck-doc repair alive during shutdown. Consume cancellation in\nrepair retry loops and lock the integrated ServiceManager path\nwith regressions so shutdown fails fast instead of drifting.
* perf(metadata): reduce sqlite lock contention
* perf(metadata): flatten batch content retries
* fix(daemon): align shutdown wait budgets
A low shutdown timeout override could expire before ServiceManager\nfinished its 5s+30s WorkCoordinator join path. Share the join\nbudget constants, clamp graceful lifecycle waits to that floor,\nand lock the behavior with a daemon regression.
* perf(metadata): bound feedback write waits
* perf(metadata): prep batch content before tx
* fix(daemon): honor no-embeddings tasks
Post-ingest queue tasks dropped the per-task noEmbeddings flag,\nso focused extraction tests still emitted embed jobs and Windows\nCI exercised extra async paths. Preserve the flag through the bus,\nskip embed dispatch when requested, and wake the extraction poller\nimmediately after successful queueing.
* perf(daemon): batch fallback metadata writes
* feat(perf,docs): optimizations for metadata writes, prompt updates and test improvements
* perf(metadata): flatten insert retries
* fix(metadata): clear CI portability blockers
Use the shared portable ScopedEnvVar in metadata search-query helper tests, add mutators for test reuse, and normalize Statement::bindAll integral dispatch so long long arguments bind consistently across platforms. Add focused regression coverage for the bindAll long long path.
* perf(metadata): batch writes and steady bench
* fix(daemon): skip inactive post-ingest pollers
* perf(metadata): tighten tag and path caches
* perf(metadata): cache small batch upserts
* fix(daemon): harden embedded host teardown
* feat(docs): updating docs policies and language
* perf(metadata): tune doc update retries
* perf(metadata): bound download retries
* perf(metadata): bound download metadata waits
* bench(metadata): scope post-ingest content path
* fix(daemon): export embedded test hooks
* fix(daemon): harden test helper linkage
* fix(build): add missing standard includes
* 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
* fix(storage): add MutexPool and hash-length precondition assertions
* fix(storage): add reference counter lifecycle assertions
- YAMS_PRECONDITION on increment size constraints
- YAMS_DCHECK on decrement zero-row detection
- YAMS_ASSERT on transaction AUTOINCREMENT ID
- YAMS_PRECONDITION on transaction active guard
- YAMS_POSTCONDITION on commit/rollback state
* fix(storage): add atomic-write and store postcondition assertions
* fix(ingestion): add batch concurrency and accounting assertions
* fix(storage): add remove counter and retrieve-read DCHECKs
* fix(daemon): add WorkCoordinator double-start precondition
* bench(storage): add store/retrieve throughput microbenchmark
* fix(daemon): replace WorkCoordinator double-start throw with precondition
* test(daemon): add fork-based double-start precondition test
* test(ingestion): add batch concurrency edge-case tests
* fix(storage): remove overly-aggressive decrement DCHECK, fix transaction test
* test(daemon): fork-based precondition test — known Catch2 SIGABRT artifact
Catch2 v3.12.0 signal handler catches child SIGABRT via abort(),
marking test as FAILED even though CHECK passes correctly.
Affects all fork-based assertion tests. Test logic is correct.
* refactor(test): remove duplicate fork test, defer to assert_catch2
* fix(review): downgrade transactionId to DCHECK, use unique benchmark hashes
* fix(review): document PRECONDITION+throw pattern, downgrade exists() to DCHECK
* test(ingestion): add maxConcurrent early-return branch coverage
* perf(storage): eliminate zero-init in retrieveRaw, fix benchmark build
retrieveRaw bottleneck: 73% of samples in vector<std::byte>(N) zero-init
that gets overwritten by file.read(). Use make_unique_for_overwrite (C++20)
to allocate uninitialized, then assign into vector.
Before/after (TSan, 1MB Retrieve): 41.7ms -> 9.0ms (4.6x faster)
Also fix Google Benchmark build: add benchmark_main_dep (provides main())
to all 7 benchmark targets. Fix storage benchmark to use valid hex hashes.
0 assertion violations across all benchmark runs.
* perf(storage): skip redundant temp-dir check, use hex table for names
Two micro-optimizations in getTempPath() hot path:
1. Drop ensureDirectories() call — temp dir already created at ctor,
stat() on every store was wasted work.
2. Replace 16 fmt::format("{:x}") calls with pre-computed hex char
table + push_back. Avoids format machinery per store.
0 opengrep findings.
* assert(storage): DCHECK temp dir, buffer, size invariants in hot paths
Coverage for the three changed functions:
getTempPath:
- DCHECK temp dir still exists (catch external cleanup in dev/CI)
- DCHECK temp name length matches TEMP_NAME_LENGTH
atomicWrite:
- DCHECK temp file exists after successful ofstream write
retrieveRaw:
- DCHECK buffer non-null for positive file sizes
- DCHECK assigned vector size matches fileSize
All benchmarks pass with zero assertion violations (TSan + Release).
* style(storage): fmt wrap DCHECK lines
* fix(review): downgrade PRECONDITION→DCHECK for catchable throws, guard zero-size UB
getObjectPath: YAMS_PRECONDITION always aborts — throw below is dead code.
Use YAMS_DCHECK instead (aborts in dev/CI, compiles out in release so
throw fires for backward-compatible catchable std::invalid_argument).
retrieveRaw: fileSize==0 → make_unique_for_overwrite(0) may return null,
assign(null,null) is UB. Early-return empty RawObject for zero-size files.
meson.build: guard benchmark blocks with benchmark_main_dep.found() too.
* fix(review): drop PRECONDITION dead throw, fix test comments
reference_counter: downgrade YAMS_PRECONDITION→DCHECK for transaction
active_ guard (aborts dev/CI, throw fires in release). Add matching
DCHECKs to decrement() and pruneReference() for consistency.
Fix inaccurate test comments claiming fork-test coverage for
WorkCoordinator double-start invariant.
* fix(review): DCHECK store postcondition, cast fileSize, rm dup main
store: downgrade YAMS_POSTCONDITION→DCHECK for exists() check.
Always-on POSTCONDITION adds stat() syscall to hot store() path;
debug-only DCHECK is the correct tier.
retrieveRaw: explicit static_cast<size_t>(fileSize) in assign
to avoid signed/unsigned narrowing warnings.
meson.build: remove benchmark_main_dep from metadata_query_bench_deps.
metadata_path_query_bench.cpp and tree_list_filter_bench.cpp both
define BENCHMARK_MAIN() — linking benchmark_main would be duplicate.
WorkCoordinator.h: update @throws→@pre in doxygen comment to match
YAMS_PRECONDITION(!started_) behavior.
* fix(bench): move pre-store to SetUp, PauseTiming unreliable
PauseTiming before first benchmark iteration caused single-iteration
runs in some Google Benchmark versions. Move pre-store into Fixture::SetUp
where it runs outside the timing loop naturally.
* fix(bench): check store/retrieve results, fix comment copy-vs-move
SetUp: throw if pre-store fails instead of silently continuing.
Retrieve: SkipWithError if retrieveRaw returns error.
Comment: assign() copies, not moves — fix misleading wording.
* fix(bench): rm benchmark_main_dep from targets with own main
ingestion_e2e_bench, retrieval_quality_bench, fusion_strategy_experiment
all define their own main() — linking benchmark_main_dep would cause
duplicate symbol at link time.
* fix(test): rename work_coordinator section, no longer tests double-start
Section title "Rejects start when already running" implied
double-start coverage but only checked worker count after first
start. Renamed to "Starts with correct worker count".
* test(refcount): add closed-state throw coverage for increment/decrement
After commit, increment/decrement must fail:
- Dev/CI (DCHECK): YAMS_DCHECK aborts, covered by fork tests
- Release (NDEBUG): DCHECK compiles out, throw fires
Conditional REQUIRE_THROWS_AS for release path.
* fix(bench): split meson guard for own-main vs benchmark_main targets
Targets with BENCHMARK_MAIN (metadata_path_query, tree_list_filter,
retrieval_quality, fusion_experiment, ingestion_e2e) only need
benchmark_dep. Storage/retrieval benchmarks need benchmark_main_dep.
Split into two guarded blocks to avoid skipping own-main targets
when benchmark_main is unavailable.
* fix(refcount): downgrade increment size PRECONDITION to DCHECK+error return
compressedSize>0 and uncompressedSize>=compressedSize come from user
content (block sizes). PRECONDITION would abort the process on corrupted
or malicious blocks. Return ErrorCode::InvalidArgument instead so
callers can handle gracefully.
* fix(daemon): defer startup maintenance
Make metadata repository readiness the startup boundary while moving search build, recovery cleanup, salvage, and VACUUM into coordinated background or pre-publication paths.\n\nKeep status honest for operators by separating database readiness from maintenance phase and surfacing recovery artifacts.
* 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
