`insertEdge` has always used `INSERT OR IGNORE`, but the edges table carried
no UNIQUE constraint — only an autoincrement PK and non-unique indexes — so
`OR IGNORE` had nothing to conflict on and behaved like a plain INSERT.
Whenever two extraction/resolution passes emitted the same edge (e.g. a
return type captured by both a type-reference and a value-reference pass),
the graph stored byte-identical duplicate rows: ~527 on this repo, inflating
edge counts and letting callers/impact list the same relationship twice.
Add a UNIQUE identity index on (source, target, kind, IFNULL(line,-1),
IFNULL(col,-1)) — in schema.sql for fresh databases and migration v6 (dedup
existing rows, then create the index) for existing ones. IFNULL folds the
nullable line/col so coordinate-less edges (synthesized / file-level) dedup
too; SQLite otherwise treats each NULL as distinct. Distinct call sites
(same source/target/kind, different line/col) are preserved — only
byte-identical structural duplicates collapse. This is the storage-layer
invariant the reporter identified: it makes OR IGNORE keep its promise and
catches every double-emit, present and future, rather than chasing each
emitting pass.
Migration v6 is deterministic (keeps the lowest id per identity group) and
idempotent (IF NOT EXISTS index; no-op DELETE once unique). The DELETE's
GROUP BY matches the index expression exactly so creation can't fail on a
leftover pair.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
deleteResolvedReferences bound every id into a single unbounded
`IN (...)`, so a list longer than SQLITE_MAX_VARIABLE_NUMBER (32766 on
the bundled node:sqlite) threw "too many SQL variables" — the one IN-list
in queries.ts that #540 missed. It's reachable only through the exported
QueryBuilder (library use): the internal resolution path uses
deleteSpecificResolvedReferences, which binds per-row and is immune, so
the CLI/MCP indexing pipeline was never affected. Wrap it in the same
SQLITE_PARAM_CHUNK_SIZE loop every sibling query uses, and add a
regression test (33k ids, past the real 32766 ceiling) that throws
without the fix.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* perf(resolution): resolve imports to definitions, not sibling import nodes (#915)
"Resolving refs" crawled (tens of minutes) on large projects — most painfully
ones mixing a big front-end and back-end. An external package or module imported
across hundreds/thousands of files (react, a shared UI package, Python
logging/typing) is re-declared as an `import` node in every importing file, so
its unresolved import ref fell through to the exact-name matcher, which scored
all K same-named import nodes via findBestMatch — K refs x K candidates = O(K^2)
per package, producing only meaningless import->import edges.
Fix: exclude `import`-kind nodes as name-match targets (they're statements, not
definitions; real import->definition resolution is the import resolver's job).
Plus two safe constant-factor wins in findBestMatch: hoist the per-candidate
ref.filePath split, and skip cross-language candidates when a same-language one
exists (provably the same winner — same-language scores >=50, cross-language
maxes at 35).
Measured: superset (Py+TS) candidates scored 7.5M -> 833K (9x), non-import edges
preserved (+1618 now resolve to real defs), ~22K useless import->import edges
removed; kubernetes (Go) computePathProximity 37.2s -> 5.0s; synthetic 8k-file
mixed repo (K=4000) resolution 16.0s -> 1.7s. Full suite green.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* docs: correct stale better-sqlite3/wasm references to node:sqlite
The SQLite backend has been Node's built-in node:sqlite (real SQLite, WAL + FTS5,
from the bundled runtime) for a while — there is no native build step and no
node-sqlite3-wasm fallback. README and the docs site were already updated; this
catches the stragglers:
- CLAUDE.md: the src/db/ backend description and the sqlite-backend test note.
- src/db/index.ts, src/mcp/tools.ts: two code comments that still blamed "the
wasm backend" for non-WAL behavior (reworded to "when WAL isn't in effect").
Leaves tree-sitter grammar wasm (web-tree-sitter / --liftoff-only) untouched —
that's a different, still-current use of wasm.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* chore(telemetry): drop the dead sqlite_backend field (schema v2)
node:sqlite is now the only backend, so the `index` event's `sqlite_backend`
field was a constant ("native") carrying no signal — and the `install` event
never actually sent it. Remove the field and the backendKind() helper, bump the
telemetry SCHEMA_VERSION 1 -> 2, and update TELEMETRY.md + docs/design/telemetry.md.
The ingest worker is deliberately left tolerant: `index` doesn't require the
field and schema_version validates as nonNegInt(99), so v2 events ingest fine and
old clients still sending v1 + sqlite_backend keep validating too. Added a legacy
comment there explaining it's safe to drop once old-client share is negligible.
telemetry.test.ts: the assertion pinning schema_version and a stale-claim fixture
line updated 1 -> 2. All telemetry tests pass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A long-lived `serve --mcp` process opens `.codegraph/codegraph.db` and holds
the fd for its whole life. If `.codegraph/` is removed and recreated AT THE
SAME PATH while it runs — `git worktree remove <p>` + re-add, or `rm -rf
.codegraph` + `codegraph init` — the held fd points at the now-unlinked inode
and can never see the new index. The server serves the pre-removal snapshot
(renamed/removed symbols still "live", new ones missing); `codegraph sync`
can't refresh it and the CLI (a fresh process) diverges. Only a restart fixed
it — and because the daemon registry is keyed by path, a same-path recreate
routes new clients straight back to the same stale daemon, so the fix has to
self-heal inside the running process.
- DatabaseConnection records the DB file's (dev, ino) at open and exposes
isReplacedOnDisk() — a different inode now at the same path. POSIX-gated:
Windows can't unlink an open file and its st_ino is unreliable, so it never
fires there.
- CodeGraph.reopenIfReplaced() opens the live file first, then swaps the
connection + query layers IN PLACE (via the new wireLayers() helper), so
every holder of the instance (the daemon's default project, cached
projectPath connections) heals without a restart. Closing the dead handle
also frees the leaked db/-wal/-shm fds pinning the unlinked inode.
- ToolHandler.getCodeGraph calls it (freshen) before serving — one stat() per
call, a no-op unless the inode actually changed, never throws into a tool.
Tests cover isReplacedOnDisk (unchanged / replaced / absent / Windows-gated)
and an end-to-end reopen that heals a held instance after a same-path recreate
(asserts the pre-heal staleness too). Validated on macOS with a dist probe of
the raw instance and the MCP serving path; full suite green.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`storeExtractionResult` deletes a re-indexed file's nodes via `deleteFile`,
which cascades through `edges.FK ... ON DELETE CASCADE` to delete every edge
whose source OR target is one of those nodes. Edges whose source is in the
re-indexed file are re-emitted by the extractor, but edges whose source is in
a *different* (unchanged) file are not — they are silently dropped. This is
issue #899: re-indexing a callee file severs `calls`/`references` edges from
callers that import it via module-attribute access (`pkg.mod.fn(...)`), so
`codegraph callers fn` reports 0 callers for functions that have real call
sites. A docstring-only edit on the callee is sufficient to trigger it.
The bug affects every incremental path that routes through `sync()` /
`indexFile()`: `codegraph sync`, the file-watcher auto-sync (which calls
`sync()`), and the git sync hooks. `codegraph index` was already fixed by
#894 (it now clears-then-rebuilds, so it's a full re-extraction, not
incremental). `sync` remains the fast incremental path and still has the bug.
Fix: before the delete, snapshot incoming cross-file edges paired with the
target node's (name, kind). After re-inserting the file's nodes + same-file
edges, re-insert the snapshot — re-resolving each edge's target to the
re-indexed node's NEW id by (filePath, kind, name). Node ids are
`sha256(filePath:kind:name:line)`, so any line shift in the callee file (e.g.
a docstring-only edit above the symbol) changes every target id and a naive
re-insert by old id would drop them all. Matching by (kind, name) is stable
across line shifts; if the symbol was renamed/removed, no match is found and
the edge stays dropped (correct). `insertEdges` still filters to endpoints
that exist, so edges whose caller (source) was deleted are also dropped.
Regression tests in `__tests__/sync.test.ts` model the RAGFlow production
case: a `pkg/mod.py` with two callees, both called from `test/test_callers.py`
via `mod.<fn>(...)`. The first test confirms a docstring-only edit that shifts
the second callee's line preserves both incoming edges. The second test
confirms renaming a callee correctly drops its old incoming edge (no phantom
preservation against a non-existent symbol).
The per-word path fix (#745) brought the backend to parity but not above:
the project name still gave the lexically-matching stack a residual dir
match + an FTS class-name match, so a backend query that included the
project name still ranked the frontend at/above the backend.
Derive the project name from go.mod module / package.json name / repo dir,
and treat a query word matching it as non-discriminative: drop it from path
relevance and from codegraph_explore's PascalCase type-disambiguation bias
(reporter's suggestions #1/#2) — unless it's the only query word, so a bare
project-name search still scores.
Narrow by construction: the down-weighting fires ONLY when a query word
matches the derived project name (≥5 chars), so every query that doesn't
name the project is byte-identical. On the reporter's repro the backend
controllers now top a backend question that includes the project name;
queries without it, bare project-name queries, and normal symbol queries
are unchanged. Query-time only (no re-index).
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A C++ method call whose receiver is another call's result — `Foo::instance().bar()`,
`WidgetFactory::create().draw()`, `openSession()->run()`, or the same stored in an
`auto` local first — lost the receiver's type during extraction. The callee degraded
to a bare method name, so when two classes shared a method name the call silently
resolved to whichever was indexed first (or not at all), corrupting callers / impact /
trace with a plausible-but-wrong edge.
Three parts:
- Capture C++ return types (new nodes.return_type column, schema v5): the
function_definition's `type` field, normalized — smart-pointer pointee unwrapped,
void/primitives dropped.
- Preserve the inner-call receiver in extraction: a C/C++ field_expression whose
receiver is itself a call is encoded `inner().method` instead of dropping to the
bare name. Other languages keep the existing behavior.
- New resolution strategy (matchCppCallChain): infer the receiver's class from the
inner call's return type, then resolve AND validate the method on it. Handles
singletons/accessors, factories returning a different type, free-function
factories, make_unique/make_shared/new/direct construction, single-level member
chains, and namespace-qualified inner calls. A wrong inference yields no edge,
never a wrong one.
EXTRACTION_VERSION 2->3 (re-index to populate return types).
Validated on the issue repro + spdlog: node count stable (no explosion),
deterministic, and ~100 pre-existing wrong `.size()`-style edges removed.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Two environments that share one working tree — most concretely Windows
and WSL — can't safely share a single `.codegraph/`: the daemon lockfile
records a platform-specific pid + socket (named pipe vs Unix socket), and
SQLite locking across the WSL2/Windows filesystem boundary is unreliable,
so two daemons over one index risks corruption.
Add a `CODEGRAPH_DIR` env var (default `.codegraph`) that overrides the
per-project data directory name, so each environment keeps its own index
in the same tree (e.g. `CODEGRAPH_DIR=.codegraph-win` on Windows). The
name is resolved live and validated (rejects separators / `..` / absolute,
falling back to the default with a one-time stderr warning). Indexing and
file-watching now skip ANY `.codegraph-*` sibling so neither side trips
over the other's data.
Routes the previously-hardcoded `.codegraph` literals (db path, lockfile,
error log, watcher ignore, file-scan skip, installer) through the
resolver. No extraction-version bump — index content is unchanged.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Completes the cross-file dependency graph behind impact / affected / explore across all 22 supported languages and 14 web frameworks, validated on real-world repos (measured fair-coverage table added to the README). Per-language resolution + framework resolvers/synthesizers (Lua/Luau require, Shopify OS 2.0 Liquid sections, Delphi forms, Rust cross-module + Rocket macros, Swift Fluent, SvelteKit/Nuxt loader/component conventions, RN/Expo bridges). 0 cross-family false edges, full suite green (1187 passed). See #708.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Batch of small, localized fixes from an open-issue triage:
- .codegraph/.gitignore now ignores everything but itself, so the database,
daemon.pid, sockets, and logs stop showing up in git status (#492, #484)
- MCP server answers resources/list and prompts/list with empty lists instead
of -32601, clearing scary log lines in opencode/Codex (#621)
- index SAP HANA .xsjs/.xsjslib as JavaScript (#556) and TS .mts/.cts (#366)
- visit anonymous AMD/CommonJS/IIFE wrapper bodies so their inner functions and
calls are indexed instead of coming up empty (#528)
- batch the changed-file lookup so a huge first sync no longer hits
"too many SQL variables" (#540)
- list files with `git ls-files -z` so non-ASCII/CJK paths survive
core.quotepath and are no longer silently skipped (#541)
- attach Go methods on generic receivers (*T[P]) to their type (#583, RC1)
- impact no longer climbs the structural `contains` edge, so a leaf symbol
stops dragging in its sibling methods (#536)
- README: explicit `codegraph install` step, run in a new shell (#631)
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The callback/observer synthesizers loaded every function and method node into
memory at once (getNodesByKind('function'/'method')) before scanning them down
to a tiny matched subset. On a symbol-dense project that array is gigabytes, so
indexing spiked the JS heap and aborted with "JavaScript heap out of memory".
Add QueryBuilder.iterateNodesByKind (a lazy node:sqlite cursor) and stream the
synthesizer scans instead of materializing them. Parsing and reference
resolution were already bounded; only the synthesis enumeration wasn't.
Measured on 80 files x 14k functions (~1.1M nodes): peak RSS 3717 MB -> 1318 MB,
no OOM. Full suite green; synthesized edges unchanged.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* feat(go): generated-file down-rank + gRPC stub-impl bridge + trace-failure inlining
Multi-pronged fix to make codegraph competitive on Go multi-module repos
(cosmos-sdk, etcd) where it previously lost or tied. Driven by an 8-question
agent-eval audit across cobra, gin, prometheus, cosmos-sdk, and etcd: the
baseline had codegraph losing ~60% on cost on cosmos-sdk and mixed on etcd
deep cross-module flows, while winning cleanly on the single-module and
non-protobuf-heavy repos.
Diagnostics ruled OUT `go.work` parsing as the gap (prometheus crushes
without it). The actual failure modes were generated-file noise warping
disambiguation, missing gRPC interface→impl bridge in structural-typing Go,
and trace's failure path triggering 3-5 follow-up tool calls instead of
inlining the material the agent needed.
Changes:
- New `src/extraction/generated-detection.ts` — path-pattern classifier
for `.pb.go`, `.pulsar.go`, `_grpc.pb.go`, `_mock.go`, `_mocks.go`,
`mock_*.go`, `.generated.[jt]sx?`, `_pb2(_grpc)?.py`, `.pb.{cc,h}`,
`.g.dart`, `.freezed.dart`. Applied as a stable sort tiebreaker in
`findSymbol`, `findAllSymbols`, `codegraph_search` (MCP + CLI),
`codegraph_explore` file ranking, and context formatter Entry Points /
Related Symbols / Code blocks. Cosmos's `msgServer.Send` now ranks #3
instead of #9 on a `Send` search.
- New `goGrpcStubImplEdges` synthesizer in `callback-synthesizer.ts` —
detects `UnimplementedXxxServer` structs in generated files, identifies
their RPC methods (excluding `mustEmbed*` / `testEmbeddedByValue` gRPC
markers), and emits `calls` edges to the matching methods on any
non-generated struct whose method-name set is a superset. Closes Go's
structural-typing gap that the existing `interfaceOverrideEdges` (Java /
Kotlin only) couldn't bridge. 467 bridge edges on cosmos-sdk; bank's
`UnimplementedMsgServer::Send` points to `x/bank/keeper/msg_server.go`
only, not to `msgClient` siblings or mock files.
- Trace-failure rewrite (`handleTrace`) — when no static path connects
endpoints, instead of telling the agent to call `codegraph_node` (a
3-4-call fan-out), inline both endpoints' bodies (120 lines / 3600 chars
per endpoint), their callers (≤6), and callees (≤8) in one response.
- Trace endpoint-pairing improvements — scores every `from`×`to`
candidate combo by shared directory prefix and tries the best-paired
pair first (the full candidate set, not just FTS top-5). A
less-canonical-path penalty (`enterprise/`, `contrib/`, `examples/`,
`vendor/`, `third_party/`, `deprecated/`, `legacy/`) ensures the
canonical-module pair wins even when a side-experiment shares more of
its directory prefix. Find-path probe budget capped at 20 pairs.
- Test-file deprioritization in `codegraph_explore` `isLowValue` — adds
suffix patterns (`_test.go`, `_spec.rb`, `.test.ts`, `.spec.tsx`,
`Test.java`, `Spec.kt`) alongside the existing directory-style patterns.
Otherwise etcd's `watchable_store_test.go` consumes 5K chars of explore
budget that should go to the hand-written flow source.
Tests:
- New `__tests__/generated-detection.test.ts` (4 unit tests) pins the
suffix patterns.
- New "Go gRPC stub→impl synthesis" integration test suite in
`frameworks-integration.test.ts` (2 tests): positive bridge from stub
to hand-written impl, AND the precision case (don't bridge to a
generated sibling like `msgClient` in the same .pb.go).
- Full suite: 1076/1076 pass.
Empirical (post-fix, n=2 average per question):
| Repo / Q | WITH | WITHOUT | Reads (W/WO) | Time (W/WO)
|-------------------------|------------|-------------|--------------|------------
| cobra (parse cmds) | $0.27 | $0.27 | 0 / 4 | 39s / 60s
| prometheus (scrape→TSDB)| $0.63 | $0.70 | 0 / 6 | 106s/143s
| cosmos-sdk Q1 (MsgSend) | $0.41 | $0.26 | 1 / 2 | 67s / 64s
| cosmos-sdk Q2 (Delegate)| $0.47 | $0.46 | 0 / 5 | 50s / 73s
| cosmos-sdk Q3 (gov tally)| $0.34 | $0.31 | 1.5 / 3 | 54s / 76s
| etcd Q1 (Put→raft) | $0.65 | $0.78 | 0 / 4 | 98s / 129s
| etcd Q2 (watch) | $0.36 | $0.50 | 0 / 4+ | 58s / 89s
Codegraph wins on reads + time on every question. Cost is mixed: 3 clean
wins, 3 tied (within 10%), 1 stubborn cost loss on the grep-favored Q1.
Compared to baseline, the cosmos-sdk cost-gap collapsed from -60% to -15%
on average, and Q3 went from a 75% loss to a tie. Raw run artifacts in
`/tmp/cg-finalv2-*/` and `/tmp/cg-final-*/`.
Memory written at `project_go_multi_module_audit.md` for the methodology
+ before/after numbers.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(mcp): auto-inline trace in codegraph_context for flow queries
When a codegraph_context task contains a flow keyword ("trace", "from",
"reach", "flow", "propagat", "how does", "how do") AND at least two
distinct PascalCase / camelCase identifiers, internally invoke trace
between the first two extracted symbols and splice the trace body into
the context response. Conservative trigger by design: false positives
waste one graph query; false negatives just fall back to the agent
calling trace itself (existing path-proximity wiring handles either
case).
Goal: collapse the agent's typical context → trace → explore sequence
into a single context call for clear flow queries, closing the
remaining cost-overhead gap on multi-call patterns. The path-proximity
+ less-canonical-path scoring + the trace-failure-inlined-bodies
behavior already let the inline trace land on the right endpoint pair
and return enough material that no follow-up codegraph_node/Read is
needed.
Doesn't fire on:
- cobra's "How does cobra parse commands and flags?" (no PascalCase
symbols) — verified in regression run, no behavior change ($0.260
WITH vs $0.257 WITHOUT, basically tied)
- queries where the agent doesn't call codegraph_context at all
(cosmos Q1 in the audit went search → trace → node → trace → node)
Tests: 1076/1076 still pass.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(mcp): trace failure inlines TO file siblings to displace node fan-out
The cosmos-Q1 audit revealed a static-resolution gap: msgServer.Send's
*real* next hop is `k.Keeper.SendCoins` — an interface-method call on an
embedded field that tree-sitter can't resolve. The static getCallees list
for msgServer.Send is all utility/error functions (StringToBytes, Wrapf,
…). The actual flow (SendCoins → subUnlockedCoins → addCoins →
setBalance) lives entirely inside `x/bank/keeper/send.go`, which is also
where the TO endpoint (setBalance) lives.
When trace fails (no static path), inline the **top 5 functions/methods
in the destination file**, ordered by line-distance from the TO node.
This catches the flow that interface-method calls obscure — the
canonical "k.<Iface>.<Method>" pattern in Go, also relevant to Java
dependency-injection / Rails service-object dispatch / etc. where
interface dispatch hides the real call.
Conservative: only fires on trace FAILURE (no static path); the success
path is unchanged. Per-body cap (40 lines / 1200 chars), top 5 siblings.
Bookkeeps with `inlinedBodies` Set so endpoints already shown above
aren't duplicated.
Result: cosmos-Q1 — historically the most stubborn cost loss (-2.2× to
-39% across the audit) — flipped to a clean WIN: $0.257 WITH vs $0.449
WITHOUT (-43%), 34s vs 79s, 0 Reads vs 2 Reads + 5 Greps, 5 codegraph
calls vs 12. Regression-checked: prometheus, cobra, cosmos-Q2, etcd-Q1
all still WIN; Q3 is high-variance ($0.30-$0.45 range historically) and
fell within that on this run.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat: extend coverage to all supported languages, not just Go
PR review feedback: the audit was Go-driven, so the patterns I added
were Go-flavored. Extend each axis to every language CodeGraph
supports per the README, so the same improvements help Java / C# /
Python / TS / Swift / Dart projects too.
**generated-detection.ts** — Added patterns for:
- TS/JS: `.gen.[jt]sx?`, `.pb.[jt]s`, `_pb.[jt]s`, `_grpc_pb.[jt]s`
(ts-proto, gRPC-web, Apollo / GraphQL codegen, Hasura).
- Python: `_pb2.pyi` (mypy stubs from protobuf).
- C#: `.g.cs` (T4 / Razor codegen), `Grpc.cs` (protoc-gen-csharp).
- Java: `OuterClass.java` (protoc-gen-java), `Grpc.java`
(protoc-gen-grpc-java; this is where the `*ImplBase` abstract
class lives — same shape as the Go `Unimplemented*Server` stub).
- Swift: `.pb.swift` (protoc-gen-swift).
- Dart: `.pb.dart`, `.pbgrpc.dart`, `.chopper.dart`.
- Rust: `.generated.rs`.
**test-file deprioritization** (`isLowValue` in `codegraph_explore`)
— Added per-language conventions that the previous regex missed:
- Python: `test_*.py` (pytest discovery) and `*_test.py`.
- Ruby: `*_test.rb` (minitest) — `*_spec.rb` already covered.
- C#: `*Tests.cs`, `*Test.cs`, `*Spec.cs`.
- Swift: `*Tests.swift` (XCTest).
- Dart: `*_test.dart`.
**IFACE_OVERRIDE_LANGS** in `callback-synthesizer.ts`'s
`interfaceOverrideEdges` — extended from `java, kotlin` to
`java, kotlin, csharp, typescript, javascript, swift, scala`. Same
shape across these (nominal `implements`/`extends` on a class to an
interface/abstract base). Also iterates `struct` (Swift value types
conforming to a protocol) in addition to `class`. The existing
matchesSymbol-style logic and `getOutgoingEdges(..., ['implements',
'extends'])` work unchanged.
**CLAUDE.md** — Added a House rule: when the user references issues
or comments, anchor them to a date and version (last release vs.
last main commit vs. current branch tip) BEFORE concluding a fix is
incomplete. Issue #388 comments from May 25-27 were responding to
the released v0.9.5 / merged-PR-469 state — not to this branch's
in-flight work. The new rule walks through the disambiguation:
`grep -m1 '^## \[' CHANGELOG.md` for release version, `git log
--first-parent main -1` for main tip.
Tests: 1076/1076 still pass.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(mcp): tiny-repo tool gating + shorter tool descriptions
Two cumulative changes targeting the small-repo cost gap surfaced by
the cross-language audit:
1. **Tool descriptions trimmed** (~2.1KB total saved across 10 tools).
The verbose marketing prose on codegraph_context / codegraph_node /
codegraph_explore / codegraph_trace / etc. wasn't moving the agent
toward better tool choices on top of the actual usage, but it was
adding ~525 tokens of cache-creation overhead to every question.
The trimmed descriptions keep the operational hints (e.g. "Query is
a bag of symbol/file names, not a question" for explore) but drop
the redundant prose.
2. **Dynamic tiny-repo tool gating** in `ToolHandler.getTools()`. On a
project with < 150 indexed files, the MCP server only exposes the
5 core tools (search, context, node, explore, trace) instead of all
10 — the omitted callers/callees/impact/status/files tools' use
cases on a sub-150-file repo reduce to one grep anyway. The MCP
tool-defs overhead is the #1 source of cost loss on tiny repos
(~$0.10-0.15 fixed cache-creation per question); cutting 5 tools
drops that by ~50%.
Effect on ky (~25 files, the worst pre-fix offender):
- Before: $0.59 WITH vs $0.42 WITHOUT (+42% loss, n=1)
- After: $0.32 WITH vs $0.44 WITHOUT (-26%, **flipped to WIN**)
Effect on cobra/sinatra/slim (50-80 files): still cost-loss, but
the gating doesn't regress them — same call-count, same reads.
The structural lower bound on those repos is what the agent's
grep+read path costs in absolute terms (~$0.20-0.30).
Non-breaking for medium+/large repos: all 10 tools remain exposed
when fileCount >= 150.
Tests: 1076/1076 still pass.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(mcp): combined tiny-tier — smaller explore + tool gating (cobra/ky flip to WIN)
Combines the tool gating from the previous commit with a matching
explore-budget cut for projects under 150 files. The two together close
the cost gap that neither closes alone:
- Tool gating alone helped ky (WIN) but didn't move cobra/slim/sinatra
- Explore-budget cut alone helped slim slightly but regressed cobra
- COMBINED: cobra flips to WIN, ky stays a WIN, ky/cobra both clean
`getExploreOutputBudget(fileCount < 150)` returns:
maxOutputChars: 13000 (was 18000)
defaultMaxFiles: 4 (was 5)
gapThreshold: 7 (was 8)
maxSymbolsInFileHeader: 5 (was 6)
maxEdgesPerRelationshipKind: 4 (was 6)
includeRelationships: true (kept ON — cheap structural signal)
maxCharsPerFile: 3800 (unchanged — monotonic invariant w/ next tier)
This survives the cobra-regression-with-trim that the earlier
budget-only attempt suffered: with only 5 tools to choose from, the
agent doesn't fall back to extra codegraph_node calls when explore
returns less — there's no node call available.
Results on the four worst small-repo losses (combined intervention):
| Repo | Files | WITH (combo)| WITHOUT | Verdict (pre → post) |
|--------|-------|-------------|-------------|--------------------------|
| cobra | ~50 | $0.25 | $0.31 | loss → **WIN** (-19%) |
| ky | ~25 | $0.39 | $0.39 | -42% → tied |
| slim | ~80 | $0.31 | $0.24 | LOSS 31% → still LOSS |
| sinatra| ~60 | $0.30 | $0.23 | LOSS 18% → still LOSS |
sinatra/slim remain a cost-loss because their WITHOUT path is
structurally cheap (~$0.20 — fewer than 4 cheap grep+read calls).
Codegraph can't beat that absolute floor with any meaningful response.
Both still WIN on time + reads + tool-call count.
Tests: tier boundary cases updated to cover the new <150 / 150-499 /
500-4999 / 5000-14999 / >=15000 progression. Off-by-one guard updated
to include the new 149↔150 boundary. All 1076 tests pass.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(context): trim maxNodes default to 8 on tiny repos
On a <150-file project the entire repo is grep-able in one turn, so the
20-node default `codegraph_context` was paying for a graph subset that
exceeds the agent's actual question. Cutting the tiny-repo default to 8
(typical 1-3 entry points + their immediate 1-hop neighbors) reduces
the context-tool response body without hitting sufficiency on the flow
shapes small repos actually contain.
Non-breaking: the agent can still pass an explicit `maxNodes` to
override; medium+ repos (>=150 files) keep the 20-node default.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* docs(mcp): pin the empirical 5-tool gating floor for tiny repos
n=2 audit on cobra/ky/sinatra ruled out cutting below 5 tools (search +
context + node + explore + trace) on the tiny-repo tier. The smaller
3-tool gate (search + context + trace) saved ~$0.025 of prompt overhead
but the agent fell back to extra Reads to cover what codegraph_node and
codegraph_explore would have answered — net cost regression on all three
test repos (cobra 17% → 48% loss, sinatra 18% → 96% loss). Documented
inline so future tuners don't re-try this dead-end.
No behavior change beyond the comment: the 5-tool gate remains the
production setting.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* docs(mcp): pin empirical lower bound on tool gating after n=2 micro test
Tested the hypothesis that exposing FEWER tools on micro repos (<50
files) would close the cost gap. Results:
- 1-tool gate (codegraph_search only):
- ky: +44% (worse than 5-tool +30%)
- express: +107% (catastrophic — was -43% WIN with all 10)
- cobra: +126% (way worse than 5-tool +17%)
The single-tool gate forces the agent to read everything because it
can't navigate the call graph. The 5 omitted tools (context, node,
explore, trace) were doing real work that grep+Read can't replicate.
Conclusion: 5 tools (search + context + node + explore + trace) is the
empirical lower bound on the tiny-repo tier. Cutting below regresses
EVERY tested repo. The remaining ~$0.04-0.08 of structural cost overhead
on tiny repos is unavoidable without sacrificing the value codegraph
provides at that scale (which would also make WITH = WITHOUT, defeating
the install).
Comment documents the dead-ends so future tuners don't relitigate.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(mcp): iter3/iter4 — raise tool-gate to 500, sufficiency steering in context, hard-exclude low-value files
Three layered changes targeting the sinatra/slim/small-repo cost gap
that iter2's body-shrink failed to close (smaller bodies just pushed
the agent to Read instead):
1. **Tool-gate threshold 150 → 500** (`TINY_REPO_FILE_THRESHOLD`).
Sinatra (~159 files) and slim (~200 files) have the same structural
problem as cobra (
* feat(context): iter7 — core-directory boost to surface dominant-file siblings in search ranking
On projects with a single file holding the dense majority of internal
call edges (e.g. sinatra's `lib/sinatra/base.rb` at ~85% of in-file
edges), text search was favoring small focused extension files over the
core file. A small focused file like `multi_route.rb` wins on verbatim
name match + file-size normalization, burying the 1500-line core file's
longer method names (e.g. `route!` vs `route`).
Fix: detect the "dominant file" — the file whose in-file edge count is
≥3× the next candidate's — then add +25 to all results sharing its
directory prefix. This pulls the core file's siblings above
sibling-package extensions without hardcoding any repo structure.
`getDominantFile()` excludes test/spec files and generated files
(e.g. etcd's `rpc.pb.go` has 4× the in-file edges of `server.go` and
would otherwise hijack the boost toward generated protobuf stubs).
SQL pulls the top 20 candidates; path-pattern filtering handles what
SQLite LIKE can't express.
* feat(mcp): iter10+iter12 — routing manifest inline + probe-sweep harness
On small projects (<500 files) with a routing-shaped query, build a
URL→handler manifest directly from the graph (each `route` node joins to
its handler via `references`/`calls` edges) and inline the top handler
file's source. The agent gets the canonical routing answer in ONE
codegraph_context call — no need to parse framework DSL, Glob for
controllers, or chase down handler files.
The lever is "make the backend smarter so the agent doesn't have to":
- Parsing routes.rb / routes/api.php / urls.py DSL is the agent's job
in the WITHOUT arm. Codegraph already has it parsed as `route` nodes
with edges to handlers — we just project that to a manifest table.
- The handler implementations are right there in the index too; inline
the highest-handler-count file so the agent sees real code, not just
symbol names.
Results on the realworld template repos that were losing badly:
rails-rw +89% LOSS → -15% WIN (agent often answers with 0-1 tool calls)
laravel-rw +29% LOSS → +12% (tight gap)
gin-rw +30% LOSS → +23% (still loss but smaller)
flask-mb +64% LOSS → +25% (smaller gap)
The residual losses are mostly the agent's defensive read behavior on
super-cheap-WITHOUT repos (express-rw still does 4 Reads even with a
19-row manifest + service file inlined). That's an agent-side ceiling
the backend can't reach further without removing tools.
Also lands `scripts/agent-eval/probe-sweep.mjs` — a direct-MCP test
harness that runs context probes across 21 repos in ~600ms (vs ~30min
for a real claude audit). Enables rapid iteration on backend changes:
edit tools.ts / context-builder, npm run build, re-run probe-sweep,
compare signals (manifest fired? handler file inlined? response size?)
before paying for a claude run.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* fix(mcp): first tool call awaits catch-up sync (no stale rows for deleted files)
`MCPEngine.catchUpSync()` reconciles the index against the working tree
after open (catching `git pull`/`checkout`/`rebase` and any edits or
deletes made while no server was running). It was fire-and-forget — so a
tool call landing in the first ~50-300ms could race past it and serve
rows for files that no longer exist on disk. The per-file staleness
banner can't help here, because that signal is populated by the file
watcher (not by catch-up).
The fix: `catchUpSync()` now pushes its promise into `ToolHandler` via
`setCatchUpGate(p)`; the first `execute()` call awaits the gate and then
clears it. Subsequent calls pay nothing. Catch-up rejections are logged
by the engine and swallowed by the handler so a transient sync failure
never breaks tools.
Most visible on the "deleted everything between sessions" case, where
MCP previously returned stale rows pointing at non-existent files.
Validated end-to-end on a 10,640-file VS Code index: with the gate, a
codegraph_search for "ExtensionHost" against an empty (but stale-DB)
directory returns "No results found" after the catch-up drains the DB;
without the gate, the same call returns 10 stale hits.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* docs(changelog): cover small-repo retrieval tuning + auto-trace + iface-override expansion
Add entries for work that landed on this branch but wasn't yet in
[Unreleased]: tiny-repo tool gating + sufficiency steering + budget
tier, auto-inline trace in codegraph_context, routing manifest inline,
core-directory ranking boost, JVM-only interfaceOverrideEdges extended
to C#/TS/JS/Swift/Scala, and the shorter tool descriptions.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The orchestrator's per-file counter only sees extraction-phase edges, so the `X nodes, Y edges` line printed after `codegraph init -i` / `codegraph index` undercounts the graph — often by more than half on repos with heavy cross-file resolution (mall: 20 047 reported vs 45 629 actually in the DB).
Snapshot (nodes, edges) before/after the full pipeline in `indexAll` and write the true delta back to the result. New lightweight `QueryBuilder.getNodeAndEdgeCount()` is one round-trip with no per-kind breakdowns. `indexFiles` (no resolution) and `sync` (uses `nodesUpdated`, not `nodesCreated`) are unaffected.
Regression test added: `__tests__/integration/full-pipeline.test.ts > reports edgesCreated including resolution + synthesizer phases`.
Drop the no-op try/catch around insertNode.run, and lowercase the Windows
SENSITIVE_PATHS entries so validateProjectPath's case-insensitive check
actually blocks c:\windows. Adds a validateProjectPath test (POSIX +
Windows-gated); the Windows-gated case was validated on a real Windows 11 VM.
Closes#327
Batch getNodesByIds to collapse N+1 reads in graph traversal, invalidate the
insertNode LRU cache so INSERT OR REPLACE doesn't serve a stale row, and run
incremental PRAGMA optimize + passive WAL checkpoint after bulk writes.
Closes#108
* fix(db): eliminate concurrent-read "database is locked"; add node:sqlite backend (#238)
WAL + busy_timeout were already enabled, so the issue's suggested fix was a
no-op. The real causes, addressed here:
- busy_timeout is now set first (before journal_mode) and lowered 120s -> 5s,
so open-time pragmas wait out a lock instead of hanging for two minutes.
- getCodeGraph no longer opens a second connection to the default project when
a tool passes its own projectPath (the in-process lock amplifier).
- The wasm fallback (no WAL) gets a bounded read-retry on SQLITE_BUSY.
- New: node:sqlite backend, preferred over wasm, so installs whose native
better-sqlite3 build fails land on a real-WAL backend instead of no-WAL wasm.
- codegraph status / codegraph_status now report the effective journal mode, so
a lock report is triageable (wal vs delete).
- CLI hard-blocks Node < 20 to actually enforce the engines floor.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* refactor(db)!: node:sqlite is the sole backend; drop better-sqlite3 + wasm
Now that distribution will bundle a Node 24 runtime, node:sqlite (real SQLite
with WAL + FTS5) is always available. Collapse the three-backend adapter to
node:sqlite only and remove the machinery the other two needed:
- Remove better-sqlite3 (optionalDependency) and node-sqlite3-wasm (dependency).
- Remove WasmDatabaseAdapter, the named->positional param translation, the
SQLITE_BUSY read-retry, the wasm fallback banner, the backend env override,
and the native/node-sqlite/wasm selection chain.
- createDatabase now opens node:sqlite directly, with a clear error pointing at
the bundled release / Node 22.5+ when the module is absent.
- NodeSqliteAdapter.close() is idempotent and pragma() supports { simple }, to
match the better-sqlite3 behavior callers relied on.
- status (CLI + MCP) reports the single node:sqlite backend; journal-mode
diagnostics and the getCodeGraph single-connection fix are retained.
- Tests repointed off better-sqlite3 onto node:sqlite.
Net -1044 lines. Running from source now requires Node 22.5+.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(dist): self-contained bundle prototype (vendored Node + install channels)
Phase 3 of the node:sqlite migration: ship a vendored Node runtime so CodeGraph
runs with no system Node and no native build (node:sqlite is built in).
- scripts/build-bundle.sh: build a per-platform archive (official Node + dist +
prod deps + launcher). Same recipe per platform; pins Node v24.16.0.
- install.sh: curl|sh installer (no Node required) — detects os/arch, pulls the
archive from Releases, symlinks onto PATH; re-run to upgrade, --uninstall to
remove. The VPS/SSH path.
- scripts/npm-shim.js: thin launcher for the npm channel — resolves the
per-platform optionalDependency bundle and execs it, so `npm i -g` keeps
working and the real work runs on the bundled Node regardless of the user's.
- BUNDLING.md: distribution design + release-pipeline TODO (CI matrix, platform
packages, code signing, brew, retiring the Node-version gate).
Validated end-to-end: darwin-arm64 and linux-x64 bundles both run init + index +
status (Backend: node:sqlite, Journal: wal) + FTS query with NO system Node —
linux-x64 verified in a clean ubuntu:24.04 amd64 container. Release archives are
gitignored; CI will produce and upload them.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(dist): add Windows PowerShell installer (install.ps1)
The `irm … | iex` one-liner for Windows, mirroring install.sh: detect arch,
pull the matching bundle from Releases, extract to %LOCALAPPDATA%\codegraph,
add it to user PATH. Re-run to upgrade. (Windows bundle production in
build-bundle.sh is still TODO.)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(dist): release workflow + npm packaging; README/CHANGELOG for bundled distro
- .github/workflows/release.yml: manually-triggered (workflow_dispatch) release
matrix. Builds a self-contained bundle per platform on its own runner
(darwin-arm64/x64, linux-x64/arm64), publishes a GitHub Release with all
archives, and publishes the npm thin-installer (shim + per-platform packages).
Windows targets are TODO (build-bundle.sh is unix-only).
- scripts/pack-npm.sh: assemble the npm packages from built bundles — per-platform
packages tagged os/cpu + the main shim package with them as optionalDependencies
(esbuild pattern). Proven locally: npm-install the tarballs, run via the shim,
resolves the bundle and runs on the bundled Node 24 (node:sqlite / WAL).
- README: install section now leads with the no-Node one-liners (curl|sh, irm|iex)
then npm/npx; "bundled · none required" badge.
- CHANGELOG: standout headline for the self-contained release, plus Added/Changed/
Removed for the install channels, node:sqlite backend, and dropped deps.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(dist): Windows bundles + single-trigger release workflow
- build-bundle.sh: add win32-x64 / win32-arm64 targets — download Node's Windows
zip, bundle node.exe + a .cmd launcher, output a .zip. Verified structurally
(PE32+ node.exe, CRLF .cmd, portable node_modules). Since there are no native
addons, any target builds on any OS, so the whole matrix builds on one runner.
- pack-npm.sh: handle .zip bundles and win32 packages (os: win32, node.exe).
- release.yml: simplified to your spec — manual trigger reads the version from
package.json, builds all platform bundles, creates the GitHub Release with notes
pulled from CHANGELOG.md, and publishes the npm shim + platform packages.
- BUNDLING.md: Windows + build-anywhere notes; release pipeline documented.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
`codegraph_callees stage_apply::run` (and `_node`, `_impact`, ...)
returned "not found" against a repo with 7-9 sibling Rust modules,
each exporting `pub async fn run`. Two underlying issues:
1. The FTS5 query builder stripped `:` as a special char without
splitting on `::`, so `stage_apply::run` collapsed to the literal
`stage_applyrun` which matches nothing. Treat `::` as whitespace
before the strip step so both halves become FTS tokens.
2. `matchesSymbol` only understood `Parent.child` qualifiers and
relied on `qualifiedName` carrying the module path. Rust file-
level functions don't have their module name in `qualifiedName`
(it's encoded in the file path instead), so even dot-style
lookups failed. Accept `::`, `.`, `/` as separators; multi-level
forms compose; Rust `crate::`/`super::`/`self::` prefixes get
stripped before path matching. Fall back to file-path containment
when the qualified-name suffix doesn't match — `stage_apply::run`
matches a `run` in any file whose path has a `stage_apply` segment.
Also tightens the no-match branch: qualified lookups no longer fall
through to a fuzzy text match. `stage_apply::nonexistent_fn` returns
`null` instead of silently resolving to an unrelated `rollback` in
the same file.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Closes the visibility gap behind issues #138 (WASM-on-macOS) and #139
(MCP "database is locked"). `better-sqlite3` is in optionalDependencies,
so when the native build fails npm install still succeeds and the
runtime silently falls back to node-sqlite3-wasm — 5-10x slower and
without WAL, so writers block readers (which is what makes the MCP
server appear to "lock the DB" in #139). The only existing signal was
a one-line `console.warn` to stderr that MCP transports typically
swallow.
This patch does NOT change install behavior — better-sqlite3 stays in
optionalDependencies so cross-platform installs keep working. It just
makes the substitution observable + recoverable.
## Visibility (4 surfaces)
- CLI `codegraph status`: new `Backend:` line under Index Statistics.
`native` rendered green; `wasm` rendered yellow with an inline
`npm rebuild better-sqlite3` nudge. Also exposed in `--json` as
`backend: 'native' | 'wasm'`.
- MCP `codegraph_status`: new `**Backend:**` line. Native form reads
`native (better-sqlite3)`; wasm form prepends a warning glyph and
includes the full fix recipe.
- Stderr banner on fallback (`buildWasmFallbackBanner`): replaces the
bare one-line `console.warn` with a multi-line bordered banner
covering macOS + Linux fix steps and optionally appending the
native load error.
- README troubleshooting: new "Indexing is slow / MCP database is
locked / WASM fallback active" entry that walks users to the
`Backend:` line and the fix.
## Per-instance backend tracking
`createDatabase` previously set a module-level `activeBackend` global.
MCP can open multiple project DBs in one process via the
`getCodeGraph()` cache, so the global would race / overwrite. Refactor:
`createDatabase` now returns `{db, backend}`, `DatabaseConnection`
carries `private backend` and exposes `getBackend()`, and
`CodeGraph.getBackend()` is the public surface. The CLI and MCP both
call `cg.getBackend()`.
## What this does NOT fix
The root cause of users landing on WASM is environment-specific (Mac
without Xcode CLT, Node version mismatch, etc.) and not fixable in
code without changing the optionalDependencies design. The README
entry tells users what to run; `Backend: native` after rebuild is the
confirmation signal.
## Tests
New `__tests__/sqlite-backend.test.ts` (6 tests) pins the banner
recipe content (so future edits can't strip the recovery commands),
the `WASM_FALLBACK_FIX_RECIPE` constant, and per-instance
`DatabaseConnection.getBackend()` / `CodeGraph.getBackend()` reporting.
Suite: 503 → 509, all passing.
Credit to @andreinknv whose analysis on #138 (and patches on his fork
at 6d0e7a2 + 69f7001) framed the visibility approach.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Both narrow indexes are fully covered by the existing (source, kind)
and (target, kind) composites via SQLite's left-prefix scan, so
they're dead weight on every write. Empirical measurements (from the
spike script in PR #122 on a 50K-node / 250K-edge synthetic DB):
- DB size: 34.7 MB → 27.0 MB (-22.2%)
- Bulk insert (250K edges): 590ms → 431ms (1.37× faster)
- source/target lookup latency: no regression
Adds migration v4 to drop both on existing databases; fresh-DB schema
no longer creates them.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* feat(search): field-qualified queries (kind:/lang:/path:/name:) + fuzzy typo fallback
Two UX improvements that turn a free-text search into something a
real user can drive precisely.
1) Field-qualified queries.
A new query parser (src/search/query-parser.ts) splits the raw query
into structured filters and a free-text remainder:
kind:function name:auth path:src/api authenticate
becomes
{ kinds: ['function'], nameFilters: ['auth'],
pathFilters: ['src/api'], text: 'authenticate' }
Filters compose with the SearchOptions arg (intersection). Unknown
prefixes pass through as plain text so `query "TODO:"` keeps working.
Quoted values (`path:"my dir"`) handle whitespace. When the user
specifies only filters with no text, the search uses a filter-only
candidate scan instead of bailing out.
Recognised today:
kind: any NodeKind value
lang: any Language value (alias: language:)
path: case-insensitive substring of file_path
name: case-insensitive substring of node.name
2) Fuzzy fallback.
When BOTH FTS and LIKE return nothing AND the text is at least 3
chars, the resolver scans the distinct-name set with a bounded
Damerau-Levenshtein-style edit distance (≤2 for ≥5 chars, ≤1 for
4-char queries, off for shorter). Bounded edit-distance early-exits
once the row min exceeds maxDist, so this stays O(distinct-names *
avg-name-length) with a very low constant.
Verified live against ollama/ollama@v0.22.0:
query "kind:function auth" → only function-kind hits
query "lang:go path:server route" → Go files under server/
query "getUssr" (typo) → finds getUser, SetUser
query "confg" (typo) → finds Config
Full test suite: 380 passed.
* fix(search): address reviewer findings — tokenizer mid-token quotes, fuzzy fan-out cap, larger filter-only over-fetch, unit tests
Five fixes from independent review:
- parseQuery tokenizer: quotes that appear MID-token (path:"my dir/
file") were not being recognised — only quotes at the start of a
token were treated as quoted spans. The fixture path:"my dir"
parsed as ['path:"my', 'dir"'] instead of ['path:"my dir"'].
Tokeniser is now a single state machine that scans into a token
until whitespace OR a quote, and recognises quotes anywhere within
the token (skips to the matching close quote).
- searchNodesFuzzy: cap the per-name follow-up SQL queries at
Math.max(limit*2, 50) AFTER edit-distance filtering. Without
this, a project with many similar names (getUser1, getUser2...)
could fan out far beyond limit queries before the inner-loop
break kicks in.
- searchAllByFilters (filter-only no-text path): bumped over-fetch
multiplier from 2× to 5× so a selective post-filter (e.g.
path:src/very/specific/file.ts) doesn't return fewer than limit
results despite the DB having matches.
- 23 new unit tests in __tests__/search-query-parser.test.ts:
parseQuery covers known-field filter, lang/language alias,
multiple kind: ORs, quoted spans (incl. mid-token), URL
passthrough, empty-value passthrough, unknown prefix passthrough,
unknown value passthrough, all-filters-no-text, empty input,
20k-char input. boundedEditDistance covers identity, single
insertion/deletion/substitution, length-difference shortcut,
empty inputs, case-sensitivity, early-exit correctness.
Full test suite: 853 passed (up from 830).
* refactor(search): derive parser kind/lang sets from types.ts as const
Convert NodeKind and Language to runtime-iterable as const arrays
(NODE_KINDS, LANGUAGES) so the query parser imports the canonical
list instead of duplicating it. Also fix the path: JSDoc to say
substring (matches the .includes() impl).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Colby McHenry <me@colbymchenry.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Removes @xenova/transformers dependency, vector storage tables, embedding generation, and semantic search APIs. Simplifies context building to use only FTS search. Eliminates visualizer server, postinstall model download, and related CLI commands. Reduces package size and complexity while maintaining core static analysis capabilities.
Uses max FTS score as baseline for exact name matches to ensure nameMatchBonus differentiation during rescoring, increases exact match limit from 5 to 20 candidates, and adds common conversational terms to stop words to reduce query noise.
Addresses cases where BM25 can bury short exact-match names (e.g. "Query") under hundreds of compound names (e.g. "QueryParserTokenManager") in large codebases, pushing them past the FTS fetch limit before post-hoc scoring can help. Supplements primary search results with direct case-insensitive name lookups for each query term, ensuring exact matches are always candidates for scoring.
Addresses cases where BFS with multiple entry points leaves most nodes disconnected after trimming. Discovers edges between already-selected nodes using specific relationship types (calls, extends, implements, references, overrides) to recover inter-node connectivity that would otherwise be lost during the node selection process.
Introduces LIKE-based substring matching to find symbols like "Search" within "TransportSearchAction" that FTS cannot match due to tokenization boundaries. Adds dedicated type hierarchy traversal to ensure parent/child classes and interfaces are included in context results, preventing BFS budget exhaustion on method-level nodes before reaching inheritance relationships.
Adds nameMatchBonus scoring to prioritize results where node names exactly or partially match query terms. Implements dedicated field extraction for Java/C# to properly categorize class fields vs variables. Optimizes BM25 search with column weights favoring name matches and increased result fetching before post-processing. Refines stop words list to preserve common programming terms like "get", "find", "list".
Improves search accuracy by boosting results when multiple query symbols appear in the same file, addressing cases where common names like "run" return too many results. Adds Go method receiver type extraction to qualified names for better searchability (e.g., "scrapeLoop.run"). Optimizes database queries with two-pass approach to handle distinctive vs common symbol names efficiently.
Replaces O(n) file scanning with O(log n) indexed database lookups by adding getAllNodeNames query and caching node lookups by name/qualified name. Pre-filters references against known symbol names to skip expensive resolution for non-existent symbols. Consolidates Go resolver helper functions into a unified resolveByNameAndKind function and moves built-in symbol sets to module-level constants for better performance.
Adds expression index on lower(name) for memory-efficient case-insensitive searches, replacing in-memory caches that caused OOM on large codebases. Includes batched reference resolution, enhanced error reporting with detailed breakdown by error type, and improved CLI progress display for scanning phases.
Java extraction:
- Handle Java method_invocation AST (receiver.method pattern)
- Support Java extends_interfaces and super_interfaces with type_list
- Create unresolved references for Java imports for cross-file resolution
- Extract interface inheritance via extractInheritance
MCP tools:
- Aggregate callers/callees/impact across ALL matching symbols (e.g. multiple
overloads or same-named methods in different classes)
- New findAllSymbols() helper for multi-symbol lookup
Graph traversal:
- Impact analysis now traverses into container children (class → methods)
so that callers of methods appear in the impact radius of their class
Other:
- Add deleteSpecificResolvedReferences() for precise cleanup after resolution
- Add 'instance-method' to resolvedBy union type
- Version bump to 0.6.8
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Eliminates anonymous error reporting functionality that was collecting stack traces and error context via Sentry. Removes all telemetry-related code, configuration options, and documentation references.
Replace native tree-sitter with web-tree-sitter + tree-sitter-wasms for
universal cross-platform support. Add node-sqlite3-wasm as a fallback
when better-sqlite3 native bindings aren't available. Move better-sqlite3
and sqlite-vss to optionalDependencies so installs never fail.
Fix installer to use npx fallback when global npm install fails, so MCP
config, hooks, and quick-start instructions all work without the bare
codegraph command in PATH.
Fix tests: update schema version expectation, fix db test paths and
method names, extract MAX_OUTPUT_LENGTH as module constant, normalize
Windows path separators in import resolver.
- Remove getNodesByIds, getNodesByKinds (zero callers)
- Remove getFileHashMap, getFileSyncMap (zero callers)
- Remove getDynamicStmt cache (only used by removed batch methods)
- Revert getStaleFiles to simple implementation (zero callers, no need to optimize)
- Remove intent field from SearchOptions (never read in search logic)
- Add provenance column on edges for tracking how edges were created
- Add project_metadata table for version/provenance tracking
- Make unresolved_refs file_path/language NOT NULL with defaults
- Add composite indexes for unresolved_refs and edges.provenance
- Update v2 migration to handle all new schema additions
- Record schema version on initialize to prevent re-migration
- Add dynamic prepared statement cache (getDynamicStmt) for varying SQL
- Add batch methods: getNodesByIds, getNodesByKinds, getFileHashMap, getFileSyncMap
- Add project metadata methods: getMetadata, setMetadata, getAllMetadata
- Optimize getStats to use single aggregate query
- Optimize getStaleFiles to use temporary table JOIN
- Add provenance parameter to getOutgoingEdges
- Add intent field to SearchOptions type
Node insertion used plain INSERT which crashes on duplicate IDs.
In large C/C++ projects, tree-sitter can produce duplicate nodes for
the same symbol (e.g. typedef struct where both struct_specifier and
type_definition resolve to the same name/kind/line, or multiple
anonymous constructs on the same line).
- Change nodes INSERT to INSERT OR REPLACE (idempotent, same data)
- Change edges INSERT to INSERT OR IGNORE (skip duplicate edges)
The node ID is sha256(filePath:kind:name:line) which already uses full
relative paths, so cross-directory collisions are not the issue.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- SQLite performance pragmas: synchronous=NORMAL, 64MB cache,
memory temp store, 256MB mmap (safe with WAL mode)
- Batch insert for unresolved refs: single transaction instead of
N individual inserts per file
- Symbol caching (warmCaches): pre-load all nodes into memory maps
before resolution, eliminating repeated SQLite queries per ref
- Async file I/O: fs.stat/readFile in indexFile() are now non-blocking
- Denormalize filePath/language onto UnresolvedReference: avoids N
node lookups during resolution, with schema migration v2
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Implements security improvements inspired by PR #16 (credit: MO2k4):
- Add validatePathWithinRoot() to prevent path traversal attacks in
extraction and context building
- Clamp MCP tool inputs (limit, depth, maxDepth) to sane ranges
- Use atomic writes (temp file + rename) for config saves
- Add symlink cycle detection in directory scanning to prevent infinite loops
- Replace all JSON.parse calls in db/queries.ts with safeJsonParse fallbacks
to handle corrupted database metadata gracefully
- Add cross-process FileLock for DB write operations (indexAll, indexFiles,
sync) to prevent concurrent writes from CLI, MCP server, and git hooks
- Remove unused path import from context/index.ts
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Adds support for Dart and Liquid languages with tree-sitter parsing.
Improves accuracy of code symbol extraction for existing languages.
Indexes project files to enhance code navigation features.
Migrates build system to facilitate code contributions.
Removes git hook functionality.
Integrates Sentry for error tracking and reporting.
Enhances project initialization and configuration loading.
- Add evaluation test suite with TypeScript and Python fixtures
- Fix MCP server to defer CodeGraph init until rootUri received
- Fix call edge extraction by calling resolveReferences() after indexAll/sync
- Fix glob matching for root-level files (e.g., **/*.py now matches auth.py)
- Fix duplicate node extraction for methods inside classes
- Update context tests to use buildContext for semantic search + graph traversal
- Export unused formatter functions to fix build
Evaluation results:
- TypeScript: 96% precision, 79% recall, 85% F1
- Python: 99% precision, 80% recall, 85% F1
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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