A truncate checkpoint started against an ACTIVE writer wins the lock and
then blocks that writer for its entire backfill; after the edge-index
recreate's multi-GB single-transaction burst that exceeds the writer's 5s
busy_timeout and fails the index with 'database is locked' (§7a.2 record
run, EXIT=1 at kernel scale — the small mid-resolution truncates folded in
ms and masked the hazard). Barrier truncates (backpressure/foldNow) are
collision-free by construction: the writer is awaiting the valve.
Dubbo gate: exit 0, peak 81MB (barrier folds carry containment), dump
byte-identical. Valve + sizing suites 27/27.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Four §7a.1 instrumented-run findings, each measured:
1. File-size trigger + truncate-at-barrier: a fully-backfilled WAL still
grows the FILE without bound — the writer only restarts at frame 0 when a
commit finds zero reader marks, which the instrumented run showed never
happens (file marched 361→721MB through two COMPLETE backfills; 22GB by
phase end). backpressure() now also trips at 4× the soft cap on raw file
size and TRUNCATEs at the parked barrier; the timer path truncates
opportunistically after complete backfills. Dubbo peak: 251MB → 69MB at
the same 16MB valve; dumps byte-identical under aggressive folding.
2. cgroup memory credit: memory.current counts reclaimable page cache — a
post-parse container read 57MB of headroom on a 6GB box and silently
disabled the pool. inactive_file is credited back (the docker-stats
working-set convention); the same run now reads a sane 4.4GB budget.
3. Pool at 2 cores reversed: sequential resolution measured FASTER than
pooled-6-on-2 at kernel scale (853s vs 1,150s), and synthesis is
Amdahl-bound by cFnPtrEdges (306s of 358s) so pooling it bought nothing.
cpuCap = min(ap−1, 6), no floor: ap=2 → sequential is the fast path.
4. Parse floor of 2: one parse worker at a 2-cpuset measured 34% slower
(493s vs 369s) — main + store-worker don't fill the second core. Floor
restores the baseline (373.5s measured).
Plus the observability §7a.1 burned three 25-minute cycles for: valve
armed/fire/timer-pass/heartbeat lines, checkpoint-worker error capture,
pool sizing decisions (incl. the disabled path), backpressure-hook
presence — all behind CODEGRAPH_SYNTH_TIMINGS / CODEGRAPH_WAL_VALVE_DEBUG.
Suite: 2,490 passed / 4 skipped (kernel required). Kernel-scale record
runs with this build follow in the migration plan §7a.1.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Three §7a.1 run-1 lessons (kernel-scale 2c/6GB: EXIT=137, WAL 22.2GB with
the backpressure hook DEPLOYED):
1. TRUNCATE at parked barriers: a completed passive backfill bounds the
un-checkpointed backlog but the FILE only stops growing when a commit
finds zero readers holding WAL marks — rare while pool workers cycle
(dubbo debug baseline: file climbed monotonically through six completed
pass-1 backfills). At a parked barrier the no-reader window is
guaranteed, so chop the file there with wal_checkpoint(TRUNCATE)
(off-thread, 2s busy_timeout — a racing reader degrades it to a no-op).
2. Futility latch: when backfill gives up (pinned reader), parking again at
every over-cap boundary burns a 20-pass checkpoint attempt — each a
worker thread + fresh connection against a multi-GB DB — per batch. Two
consecutive give-ups now disable parking for 60s; a pinned phase degrades
to pre-valve behavior instead of OOM-amplifying.
3. CODEGRAPH_WAL_VALVE_DEBUG=1 surfaces valve decisions without the
caller's verbose plumbing, and give-up lines print under
CODEGRAPH_SYNTH_TIMINGS — run 1 failed silently because give-ups were
verbose-gated.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Pool sizing used os.cpus().length, which enumerates the HOST's CPUs: inside
a 2-CPU cpuset it sized 6 resolver workers (the §7a.1 false-'sequential'
premise) and 8 parse workers, and at true 8-core concurrency six ~1GB
workers OOM-killed a 7GB container (oom_kill=5) mid-synthesis — sizing had
no memory term and no override knob.
resolvePoolSize (pure, matrix-tested): explicit CODEGRAPH_RESOLVE_WORKERS
override (0 disables, cap 16); CPU term max(2, min(availableParallelism-1,
6)) — cpuset-honest, floored at 2 so true 2-core boxes keep pooled
synthesis's ~2×; memory term floor(budget*0.7 / clamp(0.2*dbSize, 256MB,
1.5GB)) with budget = min(freemem, cgroup v2/v1 headroom). Parse pool's
core input switches to availableParallelism. Dev machines are unchanged
(still 6 workers); the 8c/7GB kernel-scale container now sizes 4.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
At kernel scale the pooled resolution/synthesis superphase grew a 22GB WAL
on a 4.6GB DB (cg1212, §7a.1): autocheckpointing is deferred for the run,
and the valve's timer-driven passive checkpoints stay perpetually partial
against the pool's continuous reads — no mechanism ever completed a
backfill, so the WAL accreted the whole phase's write volume, blowing disk
and feeding page-cache pressure into the 8-core/7GB container OOM.
The valve's writer-side backpressure() hard-cap backstop existed but was
wired only into the PARSE orchestrator. Thread it into the resolution batch
loop at the double-buffer's one pool-idle boundary (batch settled, next not
yet fanned out), after the edge-index recreate, and through the synthesis
insert loops. Parked there, the backfill completes; readers re-enter at
SQLite's backfilled mark and the next persist commit wraps the WAL.
Dubbo validation, same build: valve@16MB peak WAL 251MB (floor = the
single-transaction edge-index recreate) vs defaults 914MB; dumps
byte-identical (441,270 rows); wall unchanged (11s). Suite 2,479 green.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Python (codegraph-kernel/src/python.rs) and Go (src/go.rs) join the
native kernel, mirroring the wasm extractors bug-for-bug. Python:
decorated_definition docstrings/decorators (decorates refs only for
bare-identifier decorators — the call-kind quirk), function-in-class →
method, module-level assignments always extract as variable, from-import
per-name binding refs, self.x fn-ref candidates as bare names. Go:
receiver methods with Recv::name qualified names + contains edges to the
first earlier struct of that name, type_spec struct/interface
classification with embedding→extends and interface method nodes,
composite-literal instantiates keeping the package qualifier, top-level
var/const initializer walks attributed to the declared symbol (#693),
2-hop field chains (#1276), New().Method() re-encode (#645/#608), and
the GO_SPEC fn-ref layers.
Grammars: tree-sitter-python 0.23.6 + tree-sitter-go 0.23.4 crates, with
wasm vendored from the same tags (parser.c sha-matched) — both were
2023-era in tree-sitter-wasms.
Gates: extraction sweeps 100% (flask 83/83, django 3,035/3,038 +3
error-file deferrals, gin 99/99, prometheus 978/979 +1); full-init
dump-diffs byte-identical on flask (10,833 rows), gin (17,540), django
(360,794), and prometheus (213,758); torture fixtures enforced in npm
test. DEFAULT_ROUTED now covers typescript/tsx/javascript/jsx/java/
python/go. Full suite: 2,471 tests pass.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Kernel-routed files ship their flat tables from the parse worker to the
store worker as buffers (tryKernelExtractRaw → kernelBuffers on the
result → KernelStoreBundle); the store worker decodes and finalizes
(finalizeStoreBundle shared with the object path so filter semantics
can never drift). Files with applicable framework extract() hooks keep
the decoded path; the no-writer fallback materializes via
materializeKernelResult. Byte-identical dumps re-verified on dubbo,
excalidraw, express, gson; full suite green (2,467).
Measurement (plan §4d): dubbo's parse-loop wall is 94% store-writer
busy time — the many-core fresh-index wall is single-writer SQLite
ingest, not extraction or main-thread work. d2s improves the writer
lane ~11% (structured-clone deserialization avoided on the writer) and
frees the main thread; the remaining many-core gap is a
store-architecture arc (deferred index builds, multi-file
transactions, buffer→bind), out of the kernel project's scope.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Java joins the native kernel (codegraph-kernel/src/java.rs), mirroring
the wasm extractor's Java paths bug-for-bug: package namespaces,
imports, javadoc, annotations→decorates, type_list inheritance,
static-final constants, enum constants, anonymous classes (including
the TS side's 0-based-line quirk on the extends ref), method_invocation
calls with the this.field unwrap and the Foo.getInstance().bar() chain
encoding (#645/#608), static-member value reads, method-reference
fn-refs (#756), value-reference edges, and the full Lombok member
synthesizer (#912: Getter/Setter/Data/Value/Builder/ToString/
EqualsAndHashCode/Slf4j-family with taken-member dedup). The shared
docstring/textutil modules moved to crate level. Grammar:
tree-sitter-java 0.23.5, with the wasm grammar vendored from the same
tag (parser.c sha-matched) replacing tree-sitter-wasms' 2023-era build.
Gate (plan §4c): extraction sweeps 100% — gson 262/262, retrofit
341/341, dubbo 4,048/4,048 — plus a Java torture fixture in npm test;
full-init dump-diffs byte-identical on gson (49,766 rows), retrofit
(62,735), and dubbo (441,266 rows); all R2/R3 repos re-verified; Linux
container runs all 23 kernel tests green under CODEGRAPH_KERNEL_EXPECT=1.
The gate caught a real cross-language bug: fn-ref dedupe and value-ref
self-target checks must compare node ID STRINGS, not node-table rows —
ids collide for same-(kind, name, line) nodes, which minified one-line
bundles hit routinely (retrofit's website JS exposed it; latent in the
TS/JS walker since R2, never released). Fixed in both walkers.
Benchmark honesty: dubbo fresh-init on an 11-core Mac is ~flat
(parse-loop wall 5,020→4,394ms; total ~11.3s both arms) because that
wall is main-thread-bound (reads + store), not worker-CPU-bound — the
§6 expectation assumed otherwise. Where worker CPU binds the kernel
delivers: dubbo on a 2-CPU/6GB container drops 27.8-28.6s → 22.3-22.8s
(~1.25×). The identified lever for the many-core headline is decoding
kernel buffers directly into store rows (skipping per-node JS object
materialization); the buffer contract already carries everything.
DEFAULT_ROUTED now includes java. Full suite: 2,467 tests pass.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Gate evidence (docs/design/rust-kernel-migration-plan.md §4b):
- Graph parity, byte-identical (stronger than the §5 ≤0.5% bar): full
codegraph-init dump-diffs kernel-vs-wasm on express (13,712 rows),
excalidraw (89,898), and vscode (2,378,238 rows) — identical bytes.
Python control repo (flask) identical + timing unchanged. The parity
harness is now ORDER-sensitive (emission order drives rowids, which
drive resolution order) and dumps come from the new
scripts/dump-graph.mjs (natural keys, no rowids/timestamps).
- The one real find, caught by the vscode tier: tree-sitter error
RECOVERY is encoding-dependent — byte-identical grammar sources and
the same core (0.25.10) recover erroring files differently under
UTF-8 (native) vs UTF-16 (web-tree-sitter) parsing; proven by
reproducing the wasm tree with a native UTF-16 parse. Policy: the
kernel defers any file whose tree has_error() to the wasm extractor
(silent 'defer:' signal, per file) — parity by construction on
erroring files (incidence 0-0.42% across the gate repos), and the
harness fails if deferrals exceed 10% so a broken kernel can't hide
behind the fallback.
- Retrieval invariants: canonical excalidraw flow (mutateElement →
renderStaticScene) connects end-to-end on the kernel-indexed graph;
synthesized-edge families present. Agent A/B is vacuous under
byte-identical DBs (same justification as #1320-#1322).
- Perf: vscode init 105.4s → 82.1s (1.28×) on an 11-core Mac;
excalidraw on a 2-CPU/6GB Linux container (the CI-runner envelope)
6.2-7.1s → 4.3-4.8s (~1.5×). Linux arm64 in-container build: all 22
kernel tests green under CODEGRAPH_KERNEL_EXPECT=1. Windows VM leg
deferred (VM stopped; prlctl start needs Parallels Pro) — benign: a
missing .node falls back to wasm, and the release matrix builds and
gates the win32 prebuilds.
- Full suite: 2,465 tests pass WITH default-on routing, so the entire
extraction corpus now exercises the kernel for TS/JS wherever a
.node is staged.
DEFAULT_ROUTED = {typescript, tsx, javascript, jsx}. Override:
CODEGRAPH_KERNEL_LANGS (replaces the set) / CODEGRAPH_KERNEL=0 (kill).
Changelog entry added under [Unreleased].
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Replaces the R1 seed .scm emitter with a bespoke Rust walker
(codegraph-kernel/src/tsjs/) that mirrors TreeSitterExtractor's TS/JS
paths function-for-function: declarations (incl. #808 field/property
classification), qualified names, docstrings (#780 wrapper climbs),
signatures, imports/re-exports + per-binding refs, calls with
receiver-qualified callees (#1230 literal-receiver skip), instantiations,
decorators, inheritance, type annotations (#381), type-alias members +
tuple contracts (#359/#634), React component recognition (#841
forwardRef/memo/styled), object-of-functions / zustand-through-middleware
/ RTK Query endpoints + generated hooks / vuex + pinia store shapes,
function-as-value capture with the flush gate (#756), and value-reference
edges with the shadow prune (#895/#897). The generic query emitter is
deleted — extraction parity needs logic .scm can't express; future
languages get walkers too (migration plan §4a).
Positions and JS string-slice semantics are emitted in UTF-16 code units
natively, so kernel output is byte-identical to web-tree-sitter's — no
column diff class exists.
Parity evidence (macOS): scripts/kernel-parity.mjs (full-object multiset
diff per file) — this repo 353/353 files, excalidraw 643/643 (10,650
nodes / 10,726 edges / 68,307 refs), plus torture fixtures checked into
__tests__/fixtures/kernel-parity/ and enforced in npm test by
kernel-tsjs-parity.test.ts. The strict compare caught one real decoder
bug the loose harness missed: refs must NOT carry denormalized
filePath/language at the extractFromSource seam (the store fills them).
Perf: extraction 2.6× single-thread on excalidraw (487ms vs 1,255ms,
identical outputs). Routing stays opt-in (CODEGRAPH_KERNEL_LANGS) until
the R3 equivalence gate (large repo, DB dump-diff, retrieval invariants,
agent A/B, Linux/Windows) passes.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Phase 0 of the Rust extraction-kernel migration (docs/design/
rust-kernel-migration-plan.md, now checked in with §3a recording the
shipped state):
- codegraph-kernel/ napi-rs crate: extractFile(path, content, language)
→ five flat buffers (meta/nodes/edges/refs/arena), one JS boundary
crossing per file. Node ids computed Rust-side, byte-identical to
generateNodeId (pinned by test vector). Reserved per-node metrics slot
for the Arc 3.2 code-metrics work.
- Generic .scm-driven emitter (@def.<kind>/@name/@ref.<kind> captures,
byte-range scope stack → ::-joined qualified names, contains edges,
refs attributed to the innermost enclosing symbol). Seed TS/JS queries
are smoke-level; R2 replaces them with the full port.
- Routing seam in extractFromSource with per-file wasm fallback.
DEFAULT_ROUTED is empty — no behavior change until a language passes
its equivalence gate (R3). Dev opt-in: CODEGRAPH_KERNEL_LANGS. Kill
switch: CODEGRAPH_KERNEL=0. Loader verifies ABI + kind tables before
routing; EDGE_KINDS became a runtime array because kind order is now
wire contract.
- Grammar-source parity: vendored TS/TSX/JS wasm grammars built from the
exact crate revisions (tree-sitter-typescript v0.23.2,
tree-sitter-javascript v0.25.0, checked-in parser.c, ts-cli 0.25.10) —
the tree-sitter-wasms builds were 2023-era, which the new
kernel-grammar-parity test caught on day one. Production TS/JS parsing
gets 2.5 years of grammar fixes; full suite green (2456 tests).
- Build/release wiring: scripts/build-kernel.sh + npm run build:kernel;
release.yml kernel prebuild matrix (continue-on-error — the kernel is
optional everywhere, bundles fall back to the wasm path); bundles stage
lib/kernel/codegraph-kernel.node; release job runs the kernel suites
with CODEGRAPH_KERNEL_EXPECT=1.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Two hazards found by running today's full stack against the Linux kernel
(70,129 files) in the cg1212 repro container:
1. The parallel-synthesis fallback retried a worker-failed pass on the MAIN
thread. At multi-million-node scale a worker failure is usually a memory
ceiling, so the retry would OOM the process and take the whole index with
it. Above 1.5M nodes a failed pass is now skipped with a clear stderr
message (its synthesized edges are absent; the index completes). Below
that, the main-thread retry stays — small-scale worker crashes are
transient and the retry keeps coverage.
2. endBulkEdgeLoad rebuilt all four edge indexes in one synchronous span —
measured 79s at kernel scale, past the #850 liveness watchdog's 60s
stall window. A daemon-triggered re-index would have been SIGKILLed right
after doing the work. Now async with an event-loop yield between builds,
keeping each stall to a single index (~20s at kernel scale).
Validation: full Linux kernel index to completion in the repro container —
2,048,674 nodes / 6,405,964 edges, EXIT 0, zero passes skipped, on a 2-CPU
VM (worst case: pool disabled, sequential resolution + synthesis) in ~27min.
Phase walls: parse 6.0m, resolution 19.5m (incl. synthesis 6.3m, recreate
79s), maintenance 74s. Suite green (2444).
Also adds docs/design/native-extraction-kernel.md — the spike-validated
design for the native extraction kernel (Rust parse+walk over dubbo's Java:
202ms rayon / 1.07s single-thread vs 4.7s for the current wasm pipeline).
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The resolution persist's measured cost is B-tree maintenance on the edges
table's five indexes (offline replay of a 224k-edge resolution set: 2.8s with
all indexes, 1.1s with only the unique identity index, +0.3s to recreate the
rest). On big runs (same >=150k-ref gate as the resolver pool) the four
non-unique edge indexes are now dropped for the batch loop and recreated in
one pass each before synthesis.
Why this is safe:
- idx_edges_identity stays: INSERT OR IGNORE's dedup conflicts on it (#1034),
and its leftmost column is `source`, so the only mid-window edge reads —
resolution's supertype walks (implements/extends by source) — keep an index
via its prefix (verified with EXPLAIN QUERY PLAN).
- The window closes BEFORE synthesis, whose passes read kind-keyed, and on
every error path (finally).
- A crash inside the window heals on the next DatabaseConnection open —
schema.sql re-applies CREATE INDEX IF NOT EXISTS, same recovery as the FTS
bulk-load pattern this mirrors.
- Concurrent readers (a daemon serving the project mid-index) stay correct;
target/kind-keyed reads degrade to scans only for the window's duration.
dubbo (4,402 files): persists 4.0s -> 3.0s, fresh init 11.9s -> ~11.1s,
graph byte-identical. excalidraw (below the gate): untouched, byte-identical.
Recreation cost ~250ms, logged under CODEGRAPH_SYNTH_TIMINGS as
edge-index-recreate. Suite green (2444).
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The ~36 independent synthesis passes (callback/event/framework wiring) ran
sequentially on the indexer's main thread — 2.0s of a 4,402-file Java repo's
index, and the stage where kernel-class repos die (#1212). They now live in
an explicit registry (SYNTH_PASSES) and, when the resolver pool is alive
(>=150k-ref repos), fan out across its read-only workers: dubbo synthesis
2,024ms -> ~900ms (-55%), total fresh init 13.5s -> 11.9s. Graphs verified
byte-for-byte identical on both the pool path (dubbo) and the sequential
path (excalidraw).
Why this is safe: no pass's edges persist until the ordered merge, so every
pass sees the same committed post-resolution DB state in either mode, and
results merge in registry order regardless of completion order — the
first-seen dedup is unchanged. The pool now survives through synthesis
(destroy moved after it) instead of being torn down moments before the one
stage that could reuse it.
Robustness: a pass that fails on a worker (crash, OOM) is retried on the
main thread — a synthesizer blow-up now costs one worker instead of the
whole index, which is half the #1212 story on very large repos.
Also: ref-row cleanup deletes now run as one transaction with a cached
statement instead of one implicit commit per 500-row chunk (mechanically
fewer WAL commits; matters most on HDD-class storage). A set-based rewrite
of failed-ref parking was tried, measured ~zero on NVMe, and dropped — the
remaining persist cost is edge-index B-tree maintenance, not statement
dispatch.
SYNTH_PROGRESS_STEPS now derives from the registry (passes + fixed marks);
the pin test counts registry entries plus literal __mark sites.
Suite green (2444). Sequential-path timing unchanged on excalidraw.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Fresh init on a 4,402-file Java repo (dubbo): 18.2s -> 13.5s (-26%), with
the resolution phase going 12.6s -> 7.9s (-38%). Graphs verified
byte-identical on both the pool path (dubbo) and the sequential path
(excalidraw).
Two changes:
1. The fastInit+pool path restored WAL for the resolver workers but left
wal_autocheckpoint at its default, so the persist loop inline-checkpointed
hot pages all phase long (#1231's pathology inside resolution — measured
at 58% of resolution wall). Checkpointing is now deferred behind the
bounded valve and folded once at maintenance, mirroring the deferWal path.
2. The resolution loop is double-buffered: batch k+1 is prefetched (OFFSET
past batch k's still-pending rows, under an explicit ORDER BY rowid) and
fanned out across the pool while batch k's ref cleanup runs on the main
thread. Batch settle-waits dropped 2572ms -> 117ms.
Correctness invariant found by the byte-identical gate and now documented in
the loop: batch k+1's resolution READS batch k's edges (resolveMethodOnType
walks supertype chains over extends/implements edges that resolution itself
inserts), so edges must persist BEFORE the next batch fans out; only the ref
cleanup overlaps.
Also extends the CODEGRAPH_SYNTH_TIMINGS instrumentation with phase labels
(grammar-init, parse-loop, fts-rebuild, resolver-reinit, resolution,
callback-synthesis) and pool timings (worker open/resolve, per-batch mode,
persist), so the next profile is one env var away.
Suite green (2444). Sync path timings unchanged. Pool floor re-validated:
forced-on at 40k refs is still net-slower, so the 150k threshold stands.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Three compounding defects (#1196) made a query bag of object-literal
keys (`profileInfo isTrialEligible quotaInfo billingMethod`) return
unrelated results while the defining files never surfaced:
1. Step 5b title-cased interior humps (profileInfo -> Profileinfo) and
then compared case-SENSITIVELY, dropping every row SQLite's
case-insensitive LIKE had just recovered. The hump lookup is now
case-insensitive with an explicit uppercase-at-match requirement.
2. Step 5b/5c's kind whitelist held only type-like kinds — dead code on
method-centric codebases. Callable kinds (function/method/component)
are fetched as a SEPARATE LIKE batch so hot single-word terms can't
crowd classes out of the length-ordered 200-row batch.
3. explore's named-symbol seeding was exact-name only; a field token
seeded nothing. A camelCase token with ZERO exact defs now seeds its
camel-infix definers (callables, hump-boundary or prefix, shortest
first, capped at 3) — bare lowercase words keep the #1252 stopword
guard untouched.
The reporter's acceptance query is a pinned e2e test (definer files
present, exact-name seeding unaffected). excalidraw probe: the
canonical flow query (mutateElement renderStaticScene) is byte-
identical; NL queries shift toward more-central callables
(useUIAppState/getDefaultAppState over observer periphery).
Fixes#1196
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
`.gitignore: /repos/` lists `repos/` as ONE ignored entry, while the
CLI hint (#1156) suggests `includeIgnored: ["repos/a/", "repos/b/"]` —
the child spelling. findIgnoredEmbeddedRepos tested the opt-in matcher
against the PARENT path only, which a child pattern never matches, so
the documented opt-in silently indexed nothing and init looped the
byte-identical suggestion back at the user (#1295).
Ignored dirs that don't match as a whole are now descended (the walk
was already bounded: depth 4 / 2000 entries, and only runs when
includeIgnored is configured) and each nested repo root is matched
individually — parent spelling opts in everything under the dir, child
spelling exactly the named repos. findUnindexedIgnoredRepos gets the
same per-repo check so the hint stops nagging about repos that are
already configured while still naming unopted siblings.
Fixes#1295
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
", ".join(sorted(x)) resolved by bare name to a project function named
join — one nested inside a DIFFERENT function, so scope alone rules the
edge out. Both defects from #1230, fixed independently:
1. Extraction: a member call on a LITERAL receiver (string, number,
collection, regex — across grammars) emits no call ref at all. A
literal's methods are the language's builtins, never project
symbols; the bare-name fallback let them exact-match any same-named
project function. Silent miss, never a wrong edge.
2. Resolution: matchByExactName filters out candidates nested inside a
same-file FUNCTION container unless the ref originates within that
container's line range. Class members (parent is a class-like node),
top-level symbols, and C++ namespace prefixes (no parent node) are
untouched.
requests re-index: byte-identical (813 calls edges). excalidraw: -27
edges, all literal-receiver refs by construction. The issue's repro is
pinned: join has exactly one caller (format_fields), report_missing
has zero project callees.
Fixes#1230
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
target.conn.Exec("insert") with `conn *sql.DB` emitted a BARE `Exec`
ref (the receiver chain was dropped for non-identifier receivers), and
exact-match then bound it to the only local `Exec` — an unrelated
interface's method — fabricating an internal dependency (#1276).
Extraction now keeps Go 2-hop selector chains (`base.field.Method`),
and a dedicated matcher resolves them EXCLUSIVELY via two inference
hops: base's type from the enclosing scope (#1108 machinery), field's
declared type from the struct's own declaration lines (comment-
stripped, per-line — chi's "the tree router" doc comment otherwise
donates a phantom type). resolveMethodOnType validates the target.
Package-qualified field types are followed only when the package is
in-module — `handler http.Handler` must not bind a same-named local
decoy. Failure at any hop leaves the ref unresolved: chained Go
receivers never fall through to the bare-name strategies (they were
never emitted before, so no prior recall depends on that path).
chi before/after: node count stable (1,181); 8 correct field-chain
edges gained (mx.tree.FindRoute/InsertRoute/routes, validated,
including the unexported `node` type); the removed edges are the
prior bare-name guesses on external receivers.
Fixes#1276
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
reproStore.notifyJoinGuildStatus() after `import { reproStore }`
resolved its calls edge to the exported CONSTANT (resolvedBy:'import'),
while the identical same-file call resolved to the method via
local-variable receiver inference (#1108) — so `callers <method>`
missed every cross-file use and a widely-used method could look
unused (#1292).
resolveViaImport's member-descend now handles imported VALUES alongside
the #825 static-member case: when the base resolves to a
constant/variable, the value's type is inferred from ITS OWN
declaration lines in the exporting file (the shared #1108 pattern
table: `= new T(...)` initializers and type annotations) and the member
is resolved AND VALIDATED on that type via resolveMethodOnType. A
failed inference or validation keeps the existing constant edge —
never a fabricated one. Calls only; plain member reads still reference
the value.
excalidraw control: byte-identical graph (10,653 nodes / 19,483 calls
edges before and after).
Fixes#1292
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The CLI's bare-symbol branch passes includeCode=true to the
codegraph_node handler, but the symbol-pinned-to-file branch didn't —
so exactly when a user disambiguated an overloaded name to one file
(the point of -f), they got Location + trail with no code (#1284).
Fixes#1284
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
A directory deletion arrives as ONE event on the directory's own path.
That path has no source extension, so handleChange dropped it at the
isSourceFile gate before ever scheduling a sync — and the files inside
may never get events of their own (Windows's recursive watcher reports
only the top-most removed entry; FSEvents can coalesce a tree deletion
the same way). Every child record then sat stale in the index until an
unrelated edit happened to trigger a sync (#1285).
A non-source path that no longer EXISTS on disk now schedules the
debounced sync; the sync's scan-diff removes whatever vanished (already
correct — verified: manual `codegraph sync` cascades fine). Events for
live non-source files stay fully ignored, so build churn schedules
nothing.
Fixes#1285
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The #1242 fix (WAL deferral + checkpoint valve, the 26x win on
HDD-class storage) was wired only into indexAll. CodeGraph.sync never
touched wal_autocheckpoint, so every incremental run kept the default
1000-page cadence and re-triggered the #1231 per-page checkpoint
thrash — a 7-file sync took 2m 2s at 0-2% CPU on the reporter's
hardware, because the cost scales with the EXISTING database's hot
pages, not the change size.
sync now mirrors indexAll exactly: defer autocheckpoint + start the
valve for the run, fold the store phase's WAL before the post-store
reads, restore the interval in the finally. Same kill switch
(CODEGRAPH_NO_WAL_DEFER=1). Idle valve cost is one timer, so
watcher-frequency syncs stay cheap.
Fixes#1248
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
SEC_ATTR UINT32 LostName(VOID) — an unknown attribute macro before a
typedef'd return type — misparses in tree-sitter's C grammar: the macro
becomes the type, the return type the declarator, and the PARAMETER
LIST is stored as the function name ("(VOID)"). The C++ grammar
recovers this shape via recoverMangledCppName, but in C the real name
never reaches the mangled string, so only a pre-parse blank can help.
Attribute macros are project-specific, so the blank keys on structure:
line-leading ALL-CAPS token followed by TWO identifiers then `(` — the
`MACRO Ret name(` definition shape. Plain typedef'd returns, ALL-CAPS
calls, #define lines, multi-word builtin returns, and mid-line uses are
all rejected by construction. Offset-preserving like the C++ blanks.
curl re-index: 5,531 C functions before and after, zero name changes;
7 nodes in memdebug.c improve start-line accuracy by 1 (the macro line
no longer counts as part of the definition).
Fixes#1211
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
An out-of-line member definition inside a namespace block takes its
qualifiedName from the declarator's receiver, which is spelled RELATIVE
to the enclosing namespace — so `namespace simulator {
ManifestStartup::Output ManifestStartup::Apply(...) {} }` indexed as
ManifestStartup::Apply while the class node carried
simulator::ManifestStartup. Fully-qualified call sites
(simulator::ManifestStartup::Apply(...)) never resolved; callers and
file impact came up empty (#1291).
The receiver-based qualifiedName now composes the active namespace
prefix, anchored at the first prefix segment the receiver re-spells
(so `namespace sim { void sim::M::f() {} }` doesn't double-prefix).
namespacePrefix is only ever non-empty for C++ — Go/Rust/Kotlin/Lua
receivers pass through unchanged.
leveldb re-index: node count byte-stable (3,044), calls edges +6,
namespace-qualified method names 947 -> 1,252.
Fixes#1291
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
template<typename T> T Box<T>::get() stored qualified_name Box<T>::get —
the <T> qualifier never matched the class node indexed as Box, so the
method didn't link to its class, while the inline form of the same
method produced Box::get. ICU-shaped multi-line template parameter
lists leaked whole <…> blocks (newlines included) into qualified_name,
exceeding NAME_MAX for downstream consumers.
extractCppReceiverType now applies stripCppTemplateArgs (the #1043
normalization for base-class refs) to the receiver qualifier.
fmt re-index: template-arg-in-qualifier names 25 -> 4 (remaining are a
FMT_BEGIN_EXPORT misparse artifact and gmock conversion-operator names,
both distinct pre-existing shapes), node count byte-stable at 7,536.
Fixes#1286
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
cache.Put("a", 1), store.Get("config", out), bus.Handle("user.created",
h) — any verb-named method with a string first arg — were indexed as
HTTP routes (38 of 82 route nodes were false positives on the
reporter's 200 KLOC Go codebase). A registration's first argument must
now start with "/" (every router style), or be a Go 1.22
"METHOD /path" mux pattern on Handle/HandleFunc — which now also
extracts the real method instead of ANY.
Validated on go-chi/chi (212 real routes retained, all path-shaped)
and golang/groupcache (0 route nodes).
Fixes#1259
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
codegraph's glyphs were ASCII on every Windows console while
@clack/prompts drew its Unicode frame around them, so one index block
mixed `|` and `│` rails (#398). supportsUnicode() now mirrors the
is-unicode-supported detection clack bundles (Windows Terminal, VS
Code, ConEmu/Cmder, Alacritty, xterm-256color, JetBrains, CI), so both
systems always pick the same glyph family.
The shimmer worker's raw fs.writeSync(1) bytes still decode through the
console codepage (OEM codepages mojibake UTF-8 even under Windows
Terminal — the #168 regression to avoid), so:
- the raw path gets its own supportsUnicodeRawWrites() that stays ASCII
on win32 unless CODEGRAPH_UNICODE=1, and
- the persistent "phase done" lines move from the worker to the parent,
written via process.stdout (wide-char console API, codepage-immune) at
phase transitions — the main thread is alive there, it's delivering
the progress callback. Only transient, self-erasing animation frames
remain on the raw path, so ASCII never lands in scrollback.
Fixes#398
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
List commands (status, query, callers, callees, impact, files) embedded
ANSI color codes even when stdout was a pipe, and NO_COLOR had no effect.
One switch now decides color for all codegraph-authored output:
--no-color > --color > NO_COLOR > FORCE_COLOR > stdout TTY > CI.
Piped init/index/sync also stop emitting shimmer animation frames
(\r + erase-line rewrites) and print one plain line per phase instead;
a TTY with NO_COLOR keeps the animation but drops the color codes.
The detection mirrors picocolors' so @clack frames and our own lines
agree within a run.
Fixes#1281
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* perf(index): ~34% faster fresh indexing, byte-identical graphs
Profiling a fresh init on a medium TS repo (excalidraw, 657 files) showed
the main thread as the critical path: per-row SQLite statement calls,
repeated import-resolution walks, and per-row FTS trigger firings, with
the parse workers ~75% idle behind it. This lands the semantics-preserving
tranche of fixes:
- Multi-row batched INSERTs (nodes/edges/unresolved refs/name segments)
behind cached per-batch-size prepared statements; row order preserved,
so rowid-based resolution determinism (#1015) is unchanged.
- storeFileBundle: one transaction per file instead of four; nested
transaction() calls now flatten (BEGIN-in-BEGIN previously threw, so no
caller depended on nested rollback).
- Dedicated store-writer thread for the fresh-DB bulk path (bundles
applied in file order on a single writer connection; main thread does
no DB work during the parse loop). Kill switch: CODEGRAPH_NO_STORE_WORKER=1.
- Bulk FTS mode: drop the nodes_fts sync triggers during the bulk load,
rebuild once at the end; crash inside the window self-heals on the
next open.
- Per-context memos for resolveImportPath/findExportedSymbol + a per-file
exported-symbol index, invalidated exactly where clearCaches() already
resets the resolver's own caches.
- Fast-init on completely fresh DBs (journal in memory, no fsync until
the index completes; interrupted init re-runs from scratch). Kill
switch: CODEGRAPH_NO_FAST_INIT=1.
- MaybeYield returns undefined on the not-due path so per-ref yield
checks stop paying a promise + microtask hop each.
- Parse pool prewarm for bulk indexing; compile-cache enabled at CLI and
worker entry points.
Excalidraw fresh init: 5.11s -> 3.36s median (n=5, warm cache, M-series).
Graph dumps byte-identical across init, re-index, and sync paths; full
suite green (2403 passed).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* perf(resolution): parallel reference resolution with canonical admission
Fan resolution batches across a pool of read-only worker threads, each
hosting a full ReferenceResolver over its own SQLite connection; results
are admitted on the main thread in chunk order, so edge insertion order,
row cleanup, failure parking, and deferred post-pass queues are exactly
the sequence the single-threaded loop produces. Per-ref inputs match the
baseline because the sequential path already resolves each batch against
the state committed BEFORE that batch.
Validated byte-identical on excalidraw (pool forced on) and apache/dubbo
(4,048 Java files): dubbo full index 39s -> 19s (2.05x) with identical
graph dumps (91,495 nodes / 223,953 edges).
The pool only engages when total pending refs clear a threshold (default
150k, CODEGRAPH_PARALLEL_RESOLVE_MIN to tune, CODEGRAPH_NO_PARALLEL_RESOLVE=1
to disable): measured on a ~58k-ref repo the workers' boot CPU contends
with resolution on the same cores and makes indexing slower, so small
repos keep the sequential path. When fast-init left the DB in
memory-journal mode, WAL is restored before resolution only when the pool
will run (readers + rollback-journal writers don't mix).
Also: sqlite adapter readOnly open support.
TreeCursor spine rewrite of the body walker was built, measured neutral
on real repos and equal in a 20k-child microbench (web-tree-sitter's
namedChild(i) is not quadratic in this binding), and rejected — per-node
JS<->WASM marshaling is the floor, which a traversal swap cannot remove.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Follow-up to #1299: the per-pass bar still parked on one number while a
single long pass ran — on C-heavy repos that's the fn-pointer dispatch
pass, which sweeps every C/C++ file four times (typedefs, registrations,
field propagation, dispatch sites) and dominates the linking phase.
The pass now reports a real fraction of its dominant work
(scannedFiles / files×4, at the same per-16-files cadence as its
cooperative yield), and the orchestrator surfaces instrumented passes'
fractions as fractional steps, throttled to whole-percent movement so
the UI message volume stays bounded. The mechanism is opt-in per pass —
any synthesizer that a real repo shows parking the bar can adopt the
same callback.
Verified on the 1,342-file C repo from the report: the linking bar now
moves through 88→89→90 where it previously sat at 88 for the whole
pass; graph byte-identical (50,520 nodes / 148,232 edges).
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Two first-run UX bugs surfaced by indexing a real 1,342-file C repo:
1. After 'Resolving refs' hit 100%, the ~40 dynamic-dispatch synthesis
passes ran with no progress surface, so the bar sat frozen at 100%
long enough to read as a hang (the C fn-pointer pass alone can hold
for a while on C-heavy repos). Synthesis now reports per-pass
progress through a new 'linking' IndexProgress phase, rendered as
'Linking dynamic dispatch'. The step total is pinned by a test to
the synthesizer's actual __mark() count so adding a pass without
bumping it fails loudly.
2. node:sqlite's ExperimentalWarning is emitted once per THREAD, so the
main process plus every parse worker printed it mid-index,
interleaved with the progress UI. All launch paths now pass
--disable-warning=ExperimentalWarning: both bundle launchers, the
Windows npm-shim invocation, and the CLI self-relaunch
(NODE_RUNTIME_FLAGS, deliberately excluded from the re-exec gate so
an older installed launcher never triggers a pointless re-exec, and
version-gated off nodes older than the flag).
Verified end-to-end on the same repo: zero warnings, live linking bar,
byte-identical graph (50,520 nodes / 148,232 edges). Full suite green.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
One-time, strictly opt-in prompt at the end of codegraph install and
codegraph upgrade to join the CodeGraph Pro beta waitlist (same list as
the getcodegraph.com homepage form). Nothing is sent unless the user
answers yes AND enters an email; either answer is recorded machine-wide
so no later install or upgrade re-asks, and --yes / non-interactive / CI
runs never see the prompt.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Post-batch cleanup deleted resolved refs (and parked failed ones) by
(from_node_id, reference_name, reference_kind) — no line/col. When one
caller had several call sites to the same callee and a batch boundary
split them, the first batch's cleanup removed every row with that key,
including later-batch siblings that were never attempted — their edges
were silently never created. On nlohmann/json this ate 422 real call
edges (write_cbor's 38 to_char_type calls indexed as 11).
Refs loaded from unresolved_refs now carry their row id through
resolution, and all three persist paths (sync resolveAndPersist, the
yielding retry pass, the batched drain loop) delete / mark-failed by
exactly that id. The key-tuple methods remain only as the fallback for
hand-built refs from the public API. Failed-parking gains the same
precision: outcome can differ per call site (receiver inference reads
the ref's line), so a sibling must not inherit another row's failure.
Also untracks the zz-scratch local test files that slipped into #1268
and gitignores the pattern.
Validation: red-green regression test (5 sites, batch size 2 — old code
kept 2 edges, fix keeps 5); nlohmann/json re-index is a strict superset
of the previous edge set (0 lost, 422 recovered, spot-checked against
source).
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* fix(cpp): resolve explicit operator calls (a.operator+(b)) to the operator method (#1247)
tree-sitter-cpp can't parse an operator_name in field position: the
call_expression carries `function: <receiver>` plus an ERROR child
wrapping the operator_name instead of a field_expression callee, so the
extractor emitted a calls ref named just the receiver (`a`) and the edge
never resolved — while the operator method itself indexed fine.
Two-part fix, scoped to the explicit call form (infix `a + b` / `a[i]`
need receiver type inference and are tracked in #1258):
- extraction: recover the operator_name from the ERROR child and emit
`<receiver>.operator+` (`->` receivers normalized, `this->` emits the
bare name), like any other member call
- resolution: matchMethodCall's dot pattern now admits an operator
method part (cpp-gated; symbol chars failed the \w match), so
receiver-type inference + resolveMethodOnType validate the target —
a same-named operator on an unrelated class can't capture the edge
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(cpp): harden explicit operator-call recovery against real-world shapes (#1247)
Validated on nlohmann/json (dozens of explicit operator[] / operator* /
operator< call sites). Two refinements the synthetic fixtures missed:
- normalize spaced call-site operator names (`it.operator * ()`,
`other.operator < (*this)`) to the compact form definitions index as
- drop the ref for a complex receiver (`obj()->operator+`, member chains
ending in a call) instead of emitting a bare operator name: exact-name
fallback GUESSED among unrelated same-named operators (linked a
std::map operator[] call to an in-repo operator[]) — silent miss,
never a wrong edge
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* fix(uninstall): remove the CLI binaries too, not just agent configs (#1071)
`codegraph uninstall` swept agent configurations and stopped — every
installed binary stayed behind, so `codegraph` still ran afterward. Three
disconnected paths each removed a fraction of an installation (uninstall:
configs; install.sh --uninstall: the bundle; npm preuninstall: configs +
npm's own package), and none cleared a shadowed second install — the
uninstall edition of the #1071 PATH shadow.
The uninstall now PLANS every install present on the machine — the bundle
layout(s) (running binary's own, the platform default, a custom
CODEGRAPH_INSTALL_DIR), the npm global package (found by asking
`npm root -g`, so nvm/fnm/volta prefixes resolve correctly), and the
bin-dir launcher link (only when it verifiably points into a detected
install) — confirms with the user, then removes them all. `--yes` skips
the prompt; the new `--keep-cli` flag keeps the old configs-only behavior.
Safety rules: a source checkout is reported, never deleted; a
project-local npm install is left to the project; on unix the default
install dir doubles as the machine state dir, so only the install
artifacts (versions/, current) are removed there — telemetry choice and
daemon records survive. Windows can't delete a running exe but can rename
it (the in-place upgrade's trick): a locked node.exe is renamed aside and
surfaced as a one-file leftover instead of failing the removal, and npm
is routed through cmd.exe (a direct .cmd spawn EINVALs on modern Node).
Planner/executor are split with injected side effects (the upgrade
orchestrator's convention) and unit-tested across the shadow case,
state-dir preservation, custom dirs, foreign-shim protection, and the
locked-exe dance; validated end-to-end on macOS against a fake HOME.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(uninstall): key path math on the target platform, not the host
Real-Windows validation caught it: the planner/executor used the host
path module, so win32 fixtures were meaningless on a POSIX host and
POSIX fixtures failed on the Windows VM. Same convention as
detectInstallMethod now — path.win32/path.posix chosen by the injected
platform.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* fix(upgrade): route npm through cmd.exe on Windows — a direct npm.cmd spawn EINVALs on modern Node
Found while validating the uninstall change on the Windows VM: upgradeNpm
spawned npm.cmd without a shell, which every current Node rejects with
EINVAL (the CVE-2024-27980 hardening) — so `codegraph upgrade` on a
Windows npm install failed before doing anything. Verified live on the VM:
spawnSync('npm.cmd') → EINVAL; cmd.exe /d /s /c npm → works.
npmInvocation moves into the upgrade orchestrator (remove-binary imports
it from there — same direction as its existing imports, no cycle), and the
win32 test now pins the WORKING invocation instead of the broken one.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The recommended MCP config launches the local binary, so a server left
running drifts behind releases silently — users discover the version gap
only when something breaks. Per the reporter's preferred option 1, the
server now checks the latest GitHub release in the background on startup
(never blocking; reuses the upgrade command's release-redirect resolution
so the two can't drift) and surfaces a one-line notice on three surfaces:
one stderr line (the MCP host's server log), the initialize instructions
(with do-not-run-it-yourself guidance for the agent), and codegraph_status.
Discipline: results cache in ~/.codegraph/update-check.json shared across
every proxy/daemon on the machine — 24h TTL on success, 1h backoff after
failure, an outage never hides an already-known update, and a stale cache
re-kicks a background refresh so long-lived daemons keep noticing. The
initialize path is a memoized synchronous cache read (the respond-fast
contract holds), and both handshake answerers (session + proxy) share one
helper so they can't diverge. Never stdout.
Hardening: the latest tag arrives from a network redirect via an on-disk
cache and ends up inside agent-visible instructions, so only a canonical
vX.Y.Z rebuilt from PARSED semver fields is ever interpolated — a tag
carrying trailing text (parseSemver is not end-anchored) renders without
it, and a non-version tag renders nothing and counts as a failed attempt.
Off is off: CODEGRAPH_NO_UPDATE_CHECK=1 (dedicated) or DO_NOT_TRACK=1
(broad convention — already set by data-plane deployments) suppresses the
network call and the notice entirely. Documented in TELEMETRY.md.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
handleExplore's named-symbol seeding treats every identifier-shaped query
token as "a symbol the agent named" and grants its definition the
named-FIRST sort tier. Natural-language questions broke this assumption:
ordinary words exact-matched unrelated callables ("check" ->
WalCheckpointValve.check, "serve" -> query-worker serve, "initialize" ->
DatabaseConnection.initialize), and those collisions outranked — and within
the per-repo file budget fully displaced — the corroborated answer files,
forcing the agent back to Read/Grep. The >3-def single-pick fallback had
the same hole: on grpc, the #1064 flagship query "add a parameter to
NewClient" itself tiered balancerStateAggregator.add's file to slot #1.
Guard: a shape-precise token (camelCase, PascalCase, snake_case,
qualified) seeds unconditionally — it is an unambiguous symbol reference.
A bare lowercase word seeds only defs whose file another query token
co-names (that token is itself an exact symbol name defined in the same
file — the "check drain fire" sibling-bag shape), which an incidental
English-word collision never is. Applied by filtering cands ahead of both
branches so the overloaded-name fallback is covered too.
Validated per the retrieval playbook: deterministic probes on this repo
(collision queries fixed; sibling-bag and single-camelCase retained), and
baseline-vs-fixed probes on the #1064 repos — Alamofire and excalidraw
byte-identical, grpc improved (the add-collision file drops out and
clientconn.go + dialoptions.go lead). Full suite green.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Carries #1221 by @w0lan plus a hardening pass: property-receiver typing consults property-shaped declarations only (typed property / promoted ctor param / pseudoconstructor assignment / assignment-followed classic ctor and typed setter), so same-named locals and parameters can never mistype a property.
Co-authored-by: Roman Wolan <roman.wolan@morizon-gratka.pl>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* chore: ignore .kommandr/ directory
* fix(sync): resolve cross-file refs when an edit adds or removes the satisfying symbol (#1240)
Incremental sync scoped reference resolution to the changed files' own
refs, and a completed pass deleted every ref it failed to resolve — so
a symbol change in one file could never repair references in UNCHANGED
files, in either direction, until a full re-index:
- New-export case: a.ts imports/calls `greet` before b.ts defines it.
The failed refs were deleted at index time; when b.ts later gained
`greet`, nothing revisited a.ts — the calls/imports edges stayed
missing while status reported a clean index.
- Removal case: when a re-index (or file deletion) dropped a symbol,
the incoming edges cascade-deleted and the callers — whose resolved
refs had been consumed — never got a chance to rebind to an
alternative definition or reconnect when the symbol returned.
Fix, sharing one lifecycle:
- Schema v8: unresolved_refs gains status ('pending'/'failed') and
name_tail (last dotted segment, so `h.greet` is findable by `greet`).
Both resolver persist paths now park unresolvable refs as failed
instead of deleting them. All pending-work readers (batched drain,
non-progress guard, #1187 orphan sweep, status pendingRefs) filter to
pending, preserving their invariants and keeping status honest.
- Sync retry: after scoped resolution, failed refs whose name tail
matches a symbol name now present in the changed files are re-resolved
through a per-ref-yielding path (watchdog-safe, #1091 class). Names
matching >500 failed refs are skipped as external/builtin noise (#999
rationale).
- Removal side: createEdges stamps each resolution edge with its
originating reference (metadata.refName, + refKind when kind promotion
rewrote it). When the #899 restore misses a target or sync deletes a
file, the dropped edge is resurrected as exactly that ref — re-resolved
in the same sync (rebinding to an alternative definition) or parked
failed until the symbol reappears. Edges without the stamp (pre-upgrade,
synthesized) still drop silently: reconstructing from the target's plain
name would strip receiver context and risk a rebind a full re-index
would never make.
- Pure-removal syncs clear resolver caches so a long-lived daemon can't
resolve resurrected refs against the pre-removal graph.
Validated: issue repro now yields a graph byte-identical to a full
re-index; move/remove-readd/file-deletion scenarios all rebind or heal;
baseline-vs-new A/B on express and gin shows identical node/edge counts
and no timing regression (DB grows ~25% from the parked ref rows — pure
cache, reset by any full re-index). 8 regression tests added.
Fixes#1240
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* fix(upgrade): refresh installer-written agent surfaces after a binary upgrade
codegraph upgrade swapped the binary but never revisited what earlier
installs wrote into CLAUDE.md / AGENTS.md / GEMINI.md and the agent
configs, so sections written by a pre-1.0 installer kept teaching agents
a multi-tool surface (including tools that no longer exist) months of
releases later. The install path already self-heals everything it owns,
but nothing ever called it on upgrade.
- codegraph install --refresh: non-interactive sweep that re-runs
install() for already-configured targets only — never a first
install; permissions and prompt-hook choices are preserved.
- codegraph upgrade spawns it via the freshly-installed binary after a
successful swap (the still-running old process would only rewrite its
own stale template). Gated on PATH resolution and the
CODEGRAPH_NO_INSTALL_REFRESH=1 kill-switch; never fatal to the
upgrade.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* docs(installer): clarify refresh change reporting
---------
Co-authored-by: xuing <np2v9bvbbs@privaterelay.appleid.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Co-authored-by: Colby McHenry <me@colbymchenry.com>
Two fixes to make `codegraph upgrade` trustworthy in the terminal it ran in:
1. detectInstallMethod checked the bundle layout before the node_modules
path check, but the npm thin-installer's per-platform package IS a
complete bundle inside node_modules — so every npm install misdetected
as a standalone bundle, and upgrade curled install.sh into ~/.codegraph:
a second install that never wins the PATH race against npm's shim,
leaving `codegraph -v` permanently on the old version. Path-based
checks (_npx, node_modules) now win over layout sniffing, so npm
installs upgrade through npm again, in place.
2. After a successful swap, runUpgrade now probes the PATH-resolved
`codegraph --version` and reports the real outcome: a green
confirmation that this terminal already serves the new version, a
loud shadow warning naming the fix (`which -a codegraph`) on
mismatch, or the old soft new-terminal hint only when the probe is
inconclusive. Replaces the unconditional "open a new terminal if the
version looks unchanged" hedge. Skipped for npm-local installs, whose
binary PATH never serves.
Companion to #1239: the misdetection also broke its post-upgrade
`install --refresh` for npm users (the spawn resolved the stale shim).
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
The liveness watchdog judged the main thread by heartbeat silence alone,
which cannot distinguish a true wedge (the #850 infinite loop it exists to
kill) from one long synchronous SQLite statement on severely degraded
storage — so it SIGKILLed valid, in-progress indexes (observed on a
150-IOPS throttled rig, and latent on real HDDs at scale).
The CLI index/init paths now hand the watchdog the project's DB + WAL
paths. On a silent timeout the watchdog child stats them first: if they
advanced during the silence, the block is a slow store making forward
progress — defer and keep watching; if not, kill at the base timeout
exactly as before. Deferral is bounded by a hard cap (10× the timeout) of
continuous silence so a wedge coinciding with unrelated file activity, or
I/O hung beyond any legitimate statement, still dies. The daemon path is
unchanged (no progress paths — pure heartbeat).
Validated with real spawned processes (defer-on-progress, kill-on-static,
hard-cap kill) and on the throttled rig: a 150-IOPS index under a 10s
watchdog window — 6× tighter than production, with store stalls measured
at 10-20s — completes cleanly where the old watchdog killed it, while
true-wedge kill latency is unchanged.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Parse timeouts are now judged by the worker's own clock: the base timer
only marks a job late (after a long synchronous store stall, Node runs the
timers phase before the poll phase, so the timer fired before an
already-delivered result was processed — killing workers over parses that
took milliseconds, even on 0-byte files); a result arriving before a 3×
hard-kill backstop is accepted, timed-out files are retried, and
CODEGRAPH_PARSE_TIMEOUT_MS overrides the budget. Grammar WASM bytes are
pre-read once on the main thread and handed to every worker, so
spawns/respawns load grammars from memory instead of re-reading a
saturated disk.
Bulk indexing defers WAL auto-checkpointing for the whole run: the default
1000-page interval re-writes hot B-tree/FTS pages into the main DB file
over and over — ~95% of all disk I/O under throttled measurement. A
WalCheckpointValve bounds WAL growth with off-thread PASSIVE backfill
passes (never blocking the writer or the #850 watchdog heartbeat), pauses
the writer for a full backfill if the disk truly can't keep up, and folds
the WAL at the parse→resolution boundary so post-parse reads never page a
bulk-write-sized WAL. Opt out with CODEGRAPH_NO_WAL_DEFER=1; tune with
CODEGRAPH_WAL_VALVE_MB.
Measured at 150 IOPS (HDD class): commons-lang 1526s → 59s with 0 dropped
files (was 8); guava-scale completes in 7.6 min with a full graph where
v1.3.1 needed 25 min for a repo 5× smaller. Unthrottled: no change.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
closureCollectionEdges scanned every method/function node in every
language, but its dispatcher patterns ({ $0( / { it( ) are Swift/Kotlin
trailing-closure syntax — on PHP/JS repos the pass can never emit an
edge, yet .push(/.add( fired its append gate on nearly every function.
Per match it computed the line via src.slice(0, idx).split('\n'), which
is O(source) per match and goes quadratic on match-dense generated
functions (two-byte content roughly doubles it). On a 12,860-file
PHP/JS app that was 20+ minutes of the "Resolving refs" tail — frozen
at 97% — and a #850 watchdog kill; profiled on CRMEB it was 127s of a
166s index for zero edges.
- Skip nodes whose language isn't swift/kotlin before any file I/O.
- makeLineAt(): lazy newline index + binary search, shared with the
emitter passes' per-file lineOf.
- Yield every 256 regex matches inside the scan's match loops so a
single pathological function can't starve the watchdog.
CRMEB (ThinkPHP, 2,913 files): 166.8s -> 72.7s, graph byte-identical.
Alamofire: closure-collection edges byte-identical (9 edges, 4 fields).
Drupal core control: graph byte-identical.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
Large-codebase indexing died at the end of "Resolving refs" two ways:
watchdog kills of healthy work (24k-file Java on Windows, #1212 — third
iteration of the #1091/#1122 class) and hard OOMs (Linux kernel scale,
where v1.3.0 could not complete at any watchdog setting). Root causes:
~31 of 37 dynamic-edge synthesis passes ran start-to-finish with no
yield points, several materialized whole-graph snapshots (kotlin
expect/actual opened with getAllNodes() — 2M nodes in one array; the
C fn-pointer pass retained every C file's contents twice plus every
function node), and the post-index WAL checkpoint ran minutes of
synchronous IO on the main thread, killing even a successful index at
the finish line.
The pipeline tail now follows the same discipline as the rest: never
hold O(graph) in the heap, yield everywhere.
- All synthesis passes stream node-kind scans (cursors, not arrays) and
yield on time-budgeted checkpoints; language gates skip passes whose
filters a project's file languages provably can't satisfy.
- kotlin expect/actual filters SQL-side; c-fnptr caches are LRU-bounded,
units stream one file at a time, and the all-functions array +
write-only id map are gone; spring reads each .java once, not twice.
- runMaintenance moved to a worker thread (own SQLite connection);
per-file store commits chunk with yields behind a serialized flush
chain (preserving #1015 file-order determinism); resolver warm-up
streams the DISTINCT name set; resolution batch-tail and merged-edge
inserts run in bounded sub-transactions.
- Daemon: fixed a socket-handoff race that could leave a fresh MCP
session permanently silent (client-hello tail unshifted into a
flowing stream with zero listeners — the long-standing #662 test
flake was this real bug); first tool call no longer queues behind
the query pool's cold start (pool.ready gate).
Validation: Linux kernel (70,129 files, 2.05M nodes, 6.4M edges) fully
indexes in 27m8s on a 2-core/6GB container at default heap + default
watchdog; llvm-project (180k files) completes under 1GB RSS including
kill-and-sync recovery; synthesized-edge and full-graph parity are
byte-identical vs baseline on elasticsearch/redis/vim; the ex-flaky
daemon test passed 25/25 under load. Env-gated diagnostics kept:
CODEGRAPH_SYNTH_TIMINGS pass/phase timings, CODEGRAPH_MCP_DEBUG hop
tracing. Design record: docs/design/main-thread-stall-followup.md.
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
On a large Java/Kotlin Spring monorepo, reference resolution — not extraction —
dominated a full index (Spring Boot's ~9,650-file tree: extraction 62s,
resolution ~26min). The Spring framework resolver ran an uncached
getNodesByKind('constant') full scan + canonicalConfigKey() filter for EVERY
dotted `calls` ref (every list.add(), builder.build(), receiver.method()),
because the config-key branch gated only on "dotted java/kotlin", not on ref
kind. With ~1,100 constant nodes × ~200k dotted calls that is ~200M wasted
row-fetches/allocations.
Fixes, one theme — config-key constants bind config `references`, never `calls`:
- frameworks/java.ts: gate the Spring config-key branch on
referenceKind === 'references' (what @Value/@ConfigurationProperties emit) so
the `calls` flood skips the scan.
- name-matcher.ts: a `calls` ref no longer resolves to a yaml/properties config
node via matchByQualifiedName (service.process() vs the yaml key
service.process) — a wrong edge that also hid the real callee; it now falls
through to method resolution.
- resolution/index.ts: cache getNodesByKind in the resolver context (same
lifetime as nameCache). Fixes the same uncached-per-ref scan in the Drupal
hook_ resolver and is defense-in-depth for the Spring :prefix branch.
Measured (Spring Boot): resolution 269s→16.5s on a 4.3k-file module (16×) and
~26min→44.7s on the full 9.6k-file tree (~35×); graph byte-identical, full suite
passes. Adds a regression test (same key, two ref kinds, opposite outcomes).
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A Git super-repo whose `.gitignore` excludes its child repositories indexed
~nothing at the parent: CodeGraph respects `.gitignore` by default (#970,
#1065), so the excluded children were skipped and `codegraph init` printed
"Done" with 0 nodes — even though `init` inside each child worked fine. The
empty index was silent and unexplained.
`init`/`index` now detect the gitignored child repos they skipped when an
index comes up empty of symbols, name them, and — in an interactive terminal
— offer to index them (writing an `includeIgnored` entry to codegraph.json and
re-indexing on the spot); non-interactive runs print the exact codegraph.json
snippet to add. Gated on nodesCreated === 0, so a project that deliberately
keeps gitignored reference clones out of a working index is never nagged.
- extraction: findUnindexedIgnoredRepos — the inverse of discoverEmbeddedRepoRoots
(bounded, skips default-ignored dirs, respects existing includeIgnored)
- project-config: addIncludeIgnoredPatterns — create/merge codegraph.json,
idempotent, refuses to clobber malformed JSON
- cli: wire the detect-name-offer flow into both `init` and `index`
- tests: +13 covering detection, config writing, and the no-nag gate
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Carries #1133 forward onto current main (rebased for conflicts). A lean Unreal-Engine-style `.h` whose only C++ signal is `class ENGINE_API Foo : public Bar` (no public:/virtual/namespace/template) was misdetected as C and its class + inheritance edge silently dropped; looksLikeCpp now recognizes the export-macro-annotated class/struct shape, matching what blankCppExportMacros already recovers.
Fixes#1159.
Co-Authored-By: robertyluo <robertyluo@tencent.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Heavily-reflected UE C++ classes (`UCharacterMovementComponent`, `AActor`, `UWorld`, …) were dropped from the index: in-body no-semicolon reflection macros (`UPROPERTY`/`UFUNCTION`/`GENERATED_BODY`/`UE_DEPRECATED_*`), member-level `*_API` prefixes, and mid-line `UMETA`/`UPARAM`/`UE_DEPRECATED` accumulate tree-sitter parse errors until the enclosing class_specifier collapses into an ERROR node. Three offset-preserving, C++-only pre-parse passes (`blankCppAnnotationMacroCalls`, `blankCppApiPrefixMacros`, `blankCppInlineAnnotationMacros`) blank the markup before parsing so the class survives.
Validated on the real Epic engine headers (CharacterMovementComponent.h / Actor.h / World.h): each main class + its base clause goes from DROPPED on main to recovered with the fix.
Closes#1160.
Thanks @luoyxy for the report and root-cause analysis.
Colby Mchenry