Commit Graph
1785 Commits
Author SHA1 Message Date
Colby MchenryandClaude Opus 5.5 274b43c44b fix(python): a base imported from outside the project is not a project class of that name (#3109)
A Python class whose base the file imports from a package, like
class Color(Enum) after from enum import Enum, linked to any project class
named Enum: the import found no project file, and the name match or a framework
resolver then took the first class of that name. sqlalchemy's enums all
extended its own sql/sqltypes.py Enum, and litestar's pydantic models extended
a BaseModel in a docs example. PR #2998 extended this to parameterized bases,
like Sequence[_T] from typing.

isBoundToOutOfRepoImport is the gate that drops such an edge for JS, TS and
Rust. It now answers for Python too: the name is outside when every import
binding it is absolute and resolveImportPath, which searches for a module the
way Python does, finds none. A class in a file the import path names stays,
because that search can miss a module on a path the program sets up itself, and
so does a class of the referring file, which may rebind the name. A name no
named import binds, like one from a star import, is left as it was.

Validation:
- New python-outside-bases.test.ts: the 7 outside bases fail on main, plain and
  parameterized, and every case that must keep its edge passes both ways.
  Green here (7 passed). Taking out each of the 4 guards fails exactly its own
  test.
- A/B on 7 Python repos, 469,927 edges with the controls: 67 extends removed, 0
  added, 0 moved. All 67 read against their imports and all were wrong:
  sqlalchemy 31 (28 from enum, 3 from typing), litestar 21 (pydantic
  BaseModel), polar 14 (11 fastapi APIRoute, 2 enum IntEnum, 1 opentelemetry
  Meter), django 1 (ctypes Union).
- Controls express and gin unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 16:34:07 -05:00
danusha2345andClaude Opus 5.5 173953824d feat(sync): CODEGRAPH_SYNTH_MIN_INTERVAL_MS bounds how often live syncs rebuild the synthesized edges
A sync decides it needs the synthesized edges rebuilt when a changed file was a
synthesis input, had synthesized edges, or looks like one, and that is nearly
every TypeScript or Vue file. Those passes read the whole graph, so on a large
repo the daemon's watcher paid for a repo-wide pass on almost every edit: issue
2911 measured a 30.8 s median sync on a 36k-file monorepo. Re-synthesizing only
what changed would need every pass to work from a file subset, and they are
whole-graph scans merged in registry order.

With the variable set (whole milliseconds, 1 s to 24 h; unset, empty or out of
range means no hold), a sync within that long of the instance's last synthesis
puts the rebuild off: synthesis_pending stays set, the next sync after the
interval runs it, and a timer runs it when the interval is up even if no edit
follows. The first synthesis of an instance and a full index are never held.
Until the rebuild runs, synthesized edges can be up to the interval behind the
code, with no notice in tool output, which the maintainer accepted for 2911.

Changes on top of the contributor's commit:
- The timer's run had no error path, and an unhandled rejection ends the process
  through the fatal handlers. A database is locked at the wrong moment killed a
  real serve --mcp with exit 1, which in daemon mode is the process every session
  shares; a run outliving close() did the same with database is not open. The run
  now logs a failure and tries again after the interval, and arms nothing once
  the database is closed.
- The deferred run gets the WAL handling a sync gives the rebuild: autocheckpoint
  off with the valve running and backpressure passed down, so the commit after a
  whole graph's edges are rewritten does not checkpoint inline on the daemon's
  main thread (issues 1231 and 1248).
- The test failed on Windows with EBUSY: it ended while the run's off-thread
  maintenance held the database. It now waits for the run to finish. Holds that
  must bite use 10 s rather than 3 s so a sync on a saturated machine stays inside
  the interval, and three tests cover the failure, close and WAL paths.
- The README says what the setting costs; the changelog bullet credits the author.

Validated on four real repos, one long-lived instance per arm through six edit+sync
rounds: main, branch with the variable unset, and branch with a 60 s hold, where
synthesis_pending stayed set through all six syncs and the timer then ran.
Final graph dumps were byte-identical across all three arms on gin (19,919 lines,
311 synthesized edges), flask (11,455 lines, 3) and excalidraw (119,419 lines,
761), and nest (170,610 lines, 1,026 synthesized edges). Median sync: nest 13115 ms
to 4317 ms, excalidraw 2607 ms to 957 ms, gin 663 ms to 488 ms, flask 664
ms to 638 ms. Real serve --mcp with an outside writer holding the lock across the
timer: exit 1 before the fix; after it the server stays up, logs the failure and
the retry converges.

Original PR #2922 by @danusha2345.
Fixes #2911

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 16:13:55 -05:00
Colby MchenryandClaude Opus 5.5 fb71a9f4b3 feat(init): --local-only keeps .codegraph/ out of git entirely (#3104)
The generated `.codegraph/.gitignore` ignores everything but itself, so the
rule can be committed and shared. For someone using CodeGraph alone, that
leaves `.codegraph/` showing as untracked in `git status`, with a file to
commit that nobody else needs.

`codegraph init --local-only` makes the file the wildcard alone, so it
ignores itself too and nothing of CodeGraph's shows in git. It works on a
new project and on one that's already initialized, where it converts the
file without indexing again. Plain `codegraph init` is unchanged.

Only a file CodeGraph generated is replaced. A file with the user's own
rules is left alone, and so is a default the repository has committed,
because rewriting a tracked file would show up as a change, the opposite of
what the flag is for. Both cases say why they were left. The local-only
file carries no generated header, so every later open leaves it alone.

A flag rather than the proposed CODEGRAPH_LOCAL_GITIGNORE env var: the file
is only written when it is missing, so an env var does nothing for a
project that already has one, which is the reporter's case; an env var in a
shell profile would also silently stop every new project sharing the rule,
team repositories included. The flag is also what the issue proposed.

Validation: 22 new tests, the CLI ones against real git repositories. They
cover `git status --porcelain` staying empty, the default unchanged without
the flag, conversion leaving the database untouched, and the file surviving
sync, status, index and a plain init.

Reimplements PR 1013 by @jiangyq9.
Fixes #910

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 20:55:44 +00:00
Josh66andClaude Opus 5.5 27c904b011 fix(python): a base list wrapped over several lines is read whole
Both of the resolver's readers of a Python base list stopped early. pythonBases,
behind module-global and self. dispatch, read only the class line.
declaredSupertypes, behind class-name calls, read three lines and needed the
closing parenthesis on them. black and ruff wrap a long list one base per line,
so class Wrapped(Mixin, Base) written that way seemed to have no bases:
current = Wrapped() then current.run(), and Wrapped.run(x), reached nothing a
base declares. Extraction already read the whole list.

A new pythonBaseList reads from the class line to the list's closing
parenthesis, counting nested parentheses, within the class's extent, and leaves
out comments, so a ) in one doesn't end the list. Both readers use it.
declaredSupertypes still drops type arguments first, the composition the author
posted on PR #3001, and keeps its metaclass= and factory rewrites.

Validation:
- The test file: 7 of 9 fail without this change (the two one-line controls
  pass), 9 pass here. Putting the type-argument drop out of the merged
  case 'python' fails the new composition case and the two of PR #3083.
- Wrapped.run(None) on a wrapped base list reaches Base::run with the kernel
  and with wasm, as do a list over five lines, a decorated class, and a wrapped
  Base[Optional[User]].
- A/B on top of PR #2998, 7 Python repos, 459,440 edges: 118 added (102 calls,
  16 references), 0 removed, 959 call sites moved, 113 kept their target with
  higher confidence. requests, flask, litestar, mypy and django do not change.
  polar: 942 XRepository.from_session(session) calls move from a sibling
  repository's from_session at 0.65 to RepositoryBase.from_session at 0.85.
  sqlalchemy: wrapped heads like class Table( and class ColumnElement( now
  reach what they inherit: t.select() reaches FromClause.select. Its 17 moved
  sites read right; 15 of them land on the typing-only SQLCoreOperations
  overload of the same ColumnOperators method.
- Controls express and gin: full dumps byte-identical.
- No kernel change. Index cost with PR #2998, sqlalchemy, median of 3
  interleaved: 23.7 s on main, 25.2 s here.

Original PR #3001 by @JosefAschauer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 20:43:51 +00:00
danusha2345andClaude Opus 5.5 08b187aaf6 feat(cli): codegraph implementations <name> lists the types that implement or extend a type
Which types implement this trait is the first question when a flow crosses a
trait or interface boundary, and no command answered it: node shows members and
callers, and impact mixes implementors with dependents and tests under one list.

The command renders the shared hierarchy derivation (type-hierarchy.ts, the one
codegraph_explore and the viewer read), not a third walk. Each row gives the
kind, the edge that ties the type (implements or extends, and from depth 2 the
type it hangs off), file:line, and [test] or [synthesized]. --depth follows
subclasses of subclasses, --file narrows an ambiguous name, --json gives the
same rows. Test code is read in a new test-code.ts: the file path, a test
segment in the qualified name, and for Rust a test cfg module in the source,
since the extractor neither names such a module nor prefixes what it declares.

Changes on top of the contributor's commit:
- The command opens the index with openIndexToRead, as every other read command
  does. A plain open repairs and migrates: run during another process's bulk
  load it made the writer's next write fail with database is locked (issue
  2913), and on an older release's index a read took the schema from 4 to 16. It
  joins the read-commands test, which was red on all three scenarios.
- The Rust module reader counts braces over the existing blankRustCode instead
  of its own masker, which missed character literals, raw strings and block
  comments, so one '{' in a test module left a mock unmarked. It also reads test
  inside cfg(all(...)), the form tokio and others use.
- The README lists the command; the changelog bullet credits the author.

Validated on real repos. Across 2,761 Rust files (8,819 declarations, ripgrep,
gitbutler, lightningcss, Cap, yaak and three more) the new reader keeps all 196
test-module declarations the old one found and adds 20, spot-checked as real
fixtures in test modules. implementations ran on ripgrep (Matcher, Sink), gin
(ResponseWriter, IRouter, Binding, with Go's implicit edges marked synthesized),
flask (View at depth 2), excalidraw and Minestom. CLI start stays within 3 ms
(116 ms to 119 ms, median of 25, interleaved). The site's CLI page is left for
the release, so a push does not deploy a command nobody has yet.

Original PR #2839 by @danusha2345.
Fixes #2833

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 20:18:39 +00:00
Josh66andClaude Opus 5.5 3fca009e7b fix(python): a parameterized base links its class, like class Leaf(Base[str])
A Python class with a parameterized base had no extends edge. The grammar
parses Base[str] in a base list as a subscript, and the base-list reader took
only bare identifiers and attributes, so the base was skipped, on the wasm path
and in the kernel alike. Everything that follows the class hierarchy missed
such a class. The resolver's own text reader of a base list, pythonBases, also
looked up Base[str] verbatim and split Pair[str, int] at its inner comma, so
current = Leaf() then current.run() did not reach Base.run.

A subscript base is now unwrapped to its value before the identifier or
attribute check, in src/extraction/tree-sitter.ts and in the kernel's
python.rs. pythonBases drops bracketed type arguments before splitting the list.
Generic[T] and Protocol[T] stay outside the project like their plain forms; a
computed base, a subscript of a subscript and keyword arguments link nothing.

Validation:
- The test file runs on both arms: red on main's source and kernel (12 of 16
  fail, 6 per arm), green here (16 passed).
- Kernel parity with this kernel on 3,155 Python files of flask, requests,
  mypy, litestar, sqlalchemy, polar and django: 0 diffs, and the same 5 files
  defer to wasm as on main. The kernel and wasm edge dumps of the repos run
  both ways are identical.
- A/B against main on 7 Python repos, 457,948 edges: 1,492 added (901 extends,
  555 calls, 36 references), 0 removed, 607 call sites moved, 223 kept their
  target with higher confidence.
  polar: 491 self.get_one_or_none() style calls move from the protocol stub
  RepositoryProtocol at 0.4 to RepositoryBase and its mixin at 0.9.
  litestar: 12 calls in GenericSyncMockRepository move from
  AbstractAsyncRepository to AbstractSyncRepository.
  sqlalchemy: 435 extends and 554 calls added, like t.insert() reaching
  TableClause.insert.
  We read 44 sampled changes and every small bucket. They read right, except
  12 self.op() sites that move to the typing-only overload SQLCoreOperations.op
  and one Enum.copy that moves to TypeEngine.copy.
- 3 of the 901 extends are wrong: sqlalchemy's Sequence[_T], Tuple[int, ...]
  and MutableSet[_T] from typing link to its own classes of those names. The
  plain form does this on main (28 class X(Enum) there), and none of the 3
  brought a call edge.
- Controls express and gin: full dumps byte-identical.
- Index cost with PR #3001 on top, sqlalchemy, median of 3 interleaved: 23.7 s
  on main, 25.2 s here, with 1,143 more edges.

Original PR #2998 by @JosefAschauer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 20:05:10 +00:00
Colby MchenryandClaude Opus 5.5 9bfdd09238 feat(cli): codegraph cycles lists the files that import each other in a circle (#3099)
New `codegraph cycles [path] [--json]` prints the groups of files that
all reach each other through imports. It exits 1 when there are any and
0 when there are none, so `codegraph cycles || exit 1` works as a
pre-commit or CI check.

The command stays a thin wrapper over CodeGraph.findCircularDependencies(),
but the method itself had to change. It had no callers, and on real
repos its walk wasn't fit to print:
- It reported one list per back edge, so the number depends on the walk:
  1,490 overlapping lists on excalidraw, 87 on gin, 44 on flask.
- It left out files. A walk that meets a visited file stops there, so a
  file whose loop closes through one is never listed (now pinned by a
  test: a>b, b>a, a>c, c>b).
- It counted every edge kind, and most of the graph's edges aren't
  imports. An interface's call fans out to a test's fake, so
  src/extraction/parse-pool.ts "depended" on its own test. Two Next.js
  pages that link to each other were a cycle. gin's files were a 55-file
  knot, though Go forbids import cycles. With exit 1 those are failures
  nobody can fix.

The method now takes the strongly connected components of the file
import graph, one group per knot. The Tarjan pass moves from the
viewer's map into src/graph/file-cycles.ts and both surfaces use it, so
the viewer's "Circular imports between files" panel, which was reading
every edge too, now reports the same groups. Dependent counts on the map
keep their own edge list.

Validation: new cli-cycles and file-cycles suites, plus cycles in the
read-commands suite (mid-rebuild, and old schema indexes); 4 of the 10
findCircularDependencies and finder tests fail with main's method and
all 15 pass with this one. Against the TypeScript compiler's own module
resolver over the same files (kit oracle): excalidraw 3 groups, 369
files, all identical; codegraph's src/ 3 of 4 identical, and the fourth
needs src/resolution/name-matcher.ts, which at 1.6 MB is over the
default size limit and so isn't parsed. flask reports 2 groups and gin
none. It runs in under a second on each. Type-only imports count, as
they aren't told apart in the graph.

The MCP tool from PR #889 is left out on purpose: a new tool is rarely
picked up, and this needs no agent steering.

Reimplements PR #1012 by @jiangyq9, with the exit code from the CLI in
PR #889 by @goutham80808.

Fixes #888

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 19:53:53 +00:00
danusha2345andClaude Opus 5.5 47526d2078 feat(serve): --no-telemetry turns telemetry off for one MCP server entry
A team that shares an MCP config had no way to opt one server entry out of
telemetry without an environment variable, which not every client lets a
shared config set. Issue 1908 asked for a flag.

serve --no-telemetry sets CODEGRAPH_TELEMETRY=0 for the process, the same
chokepoint --no-watch uses for CODEGRAPH_NO_WATCH, so there is no new
telemetry code path: telemetry reads the variable on every check, and the
background daemon a server spawns inherits its environment. A daemon that is
already running keeps its own setting until it exits, which TELEMETRY.md
states; codegraph telemetry off covers every process.

Changes on top of the contributor's commit: the test spawns the server with
the WASM runtime flags, as AGENTS.md requires on Windows (without them the
re-exec'd grandchild keeps the temp dir open past the child's exit), and the
changelog bullet states the limit and credits the author.

Validated with real proxy-to-daemon runs on Windows against opted-in private
homes, reading the telemetry queue each daemon left on exit:
- a flagged client starts the daemon: nothing recorded;
- control, no flag: the tool call is recorded;
- a flagged client joins a running unflagged daemon: its call is recorded,
  the documented limit;
- an unflagged client joins a flagged daemon: nothing recorded;
- codegraph telemetry off with a daemon running: nothing recorded.

Original PR #1923 by @danusha2345.
Fixes #1908

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 19:31:16 +00:00
Colby MchenryandClaude Opus 5.5 7889da6697 feat(status): show files parsed beside files found, and add --strict (#3096)
A language's file count says what the files are, not whether anything came
of them, so a language with nothing in the graph could read as healthy.

`codegraph status` and `codegraph_status` now show how many of a language's
files yielded symbols when that isn't all of them, and warn about a language
where none did. `status --json` gains filesByLanguage,
parsedFilesByLanguage and unparsedLanguages. `status --strict` exits 1 unless
the index is finished, up to date and every language that should yield
symbols did.

The count stays out of getStats(), which every explore runs. A plain
EXISTS probe per file would have doubled getStats() on a 14,569-file index,
from about 40 ms to about 80 ms. The query status runs instead takes 4.3 ms
there, because the stored node count settles nearly every row, and only
status runs it.

The gate covers more than a zero count because a grammar that can't load no
longer leaves one: since PR 2335 nothing is stored for such a file, the
language drops out of the rows, and the only trace is pending files. A gate
checking zeroes alone would pass that.

Text changes: a language row gains "  (N with symbols)" only when the two
numbers differ, and a warning line appears for a language with no symbols.
Every other line, and every existing JSON field, is unchanged.

Across 115 real indexes, 9 repos have a code language with no symbols, all
of them stubs in languages with at most 3 files, such as ripgrep's
.nvim.lua. A file-count threshold would have hidden a real failure in a
small smoke-test project, so the rule stays plain and the warning names the
files instead.

Reimplements PR 1658 by @ferrine.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 18:53:03 +00:00
Colby MchenryandClaude Opus 5.5 f4c4dae91c feat(mcp): the server gives hosts its title and icon (#3095)
`initialize` now answers with serverInfo.title "CodeGraph" and one
embedded SVG in serverInfo.icons, on the direct path and from the
daemon proxy, which share SERVER_INFO. A host that shows them can list
CodeGraph by name and logo instead of a plain `codegraph`.

The icon is the site's favicon (site/public/favicon.svg) on a light
tile. The bare mark is dark ink on nothing, and on a dark background
only its two white dots show (checked in a browser at 16 to 64 px). It
is spelled out in the source instead of as a base64 blob, so a reader
can see it is three lines and three circles.

`sizes` is left off the icon on purpose. It's optional and says nothing
about an SVG, and @modelcontextprotocol/sdk 1.18.0 typed it as a string
where the spec settled on an array, so a host on that SDK would fail the
whole handshake on the array form.

Left out from PR #879, on purpose: `_meta.icons` and icons on every
tool. Those add about 1 KB per tool to each tools/list for no host we
could find that needs them; Codex reads serverInfo.icons.

What each host shows, read from its source or binary on 2026-10-30:
- Codex: keeps serverInfo.title and .icons and sends them to its app
  (McpServerStatus.serverInfo); the terminal UI's /mcp doesn't read them.
- opencode: reads serverInfo.title into the server list; its dialogs
  still print the config name, and it doesn't read icons.
- Claude Code 2.1.296: connects fine with these fields (checked with
  `claude mcp list` in a sandbox home), and no read of title or icons
  turns up in its binary, so it keeps showing the config name.
- Cursor: closed source and not on this machine. Its docs mention no
  server title or icon, so this is unverified.

Validation: 3 tests in mcp-initialize fail on main's session and pass
here; mcp-daemon now pins the proxy's serverInfo to the same object.

Reimplements PR #879 by @fedosov.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 18:38:45 +00:00
Colby MchenryandClaude Opus 5.5 22cf7d3aa1 fix(watch): a watch callback that throws no longer ends the host's process (#3092)
A program that uses CodeGraph as a library passes callbacks to watch().
FileWatcher.flush() runs from a timer with no caller to catch anything, and it
called onSyncError and onDegraded (through degrade()) in its catch block. A
throw from either left flush() as an unhandled rejection, which ends the host
process with exit 1. A throw from onDegraded also skipped the stop() that
degrade() owes, so a watcher reporting itself degraded kept retrying. A throw
from onSyncComplete sat inside the try, so it counted a sync that worked as a
failed one and called onSyncError with an error that was no sync failure.

All three now go through one guard, callHost(), which logs the throw as a
warning and changes nothing else. The CLI and MCP server are not affected:
their callbacks only write to stderr. Only a host's own callback can reach this.

Validation:
- Three new tests in watcher.test.ts fail on main and pass here (64/64 in the
  file). Putting each guard back one at a time fails exactly its own test.
- A host script on the public API (watch() with a throwing onSyncComplete and
  onSyncError, then a real file edit): main exits 1, this branch logs the throw
  and keeps running, exit 0.

PR #3074 listed ten lint findings; this keeps the two watcher call sites'
purpose and leaves out the rest, which change no behaviour:
- flushOrdered(): flushChain's body catches everything, so it cannot reject.
- stop() from timers and signals: nothing stop() awaits can reject today, and
  a forced rejection already exits (exit 1, one fatal line).
- await on getCodeGraph and the upgrade functions: plain values, nothing else
  runs in that microtask.
- { cause } on the rebuild and daemon-lock errors: the rebuild message already
  carries the reason, and nothing reads or prints cause.

Reimplements PR #3074 by @johnhldiver-beep. Refs issue 2643.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 18:19:56 +00:00
Colby MchenryandClaude Opus 5.5 17d5426d63 feat(files): list a project's files by the package that owns them (#3090)
Nothing could answer "which package owns this file": manifests are not
source, so they have no row in the index, and `--format grouped` groups by
language.

`codegraph files --format package` and `codegraph_files` with
`format: "package"` now group files by the nearest package.json or
composer.json above them that names a package, so a monorepo splits into
its workspace members with no configuration. The answer is read from disk
when asked, so it stays current without a re-index. A manifest that names
nothing doesn't stop the walk, and files nothing claims get a section of
their own, last. Each directory is resolved once and shares its parent's
answer. Reads are bounded by the source size limit and stay inside the
project.

Opt-in only: the default tree output and the `--json` shape are unchanged,
and `--json` keeps ignoring `--format` as it always has.

Validation: 31 new tests, including the real CLI. On vuejs/core the default
listing and `--json` are byte-identical to main. The walk over babel/babel's
28,653 files in 13,484 directories takes a median 460 ms, on the query
worker pool for `codegraph_files`.

Reimplements PR 2863 by @LuisAlbertoMK.
Fixes #1871

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 17:59:30 +00:00
Josh66andClaude Opus 5.5 cd04b21a31 fix(python): a base's type argument is no supertype, so Repo.save() is not User.save
The Python branch of declaredSupertypes read every word of a class's base
list, so class Repo(Base[User]) declared both Base and User. A call on the
class or on a receiver named after it, Repo.save() or repo.save(), walks those
supertypes for the method (classStrategyMethod to inheritedClassMethod), and
when Base declares no save it reached User.save at 0.85 or 0.8. In
class Mixed(Base[Optional[User]], Mixin) the type argument also came ahead of
Mixin, so Mixed.save() reached User.save instead of Mixin.save.

Bracketed type arguments, nested ones and quoted forward references too, are
now dropped before the names are read. The base itself is still read and
searched. Other languages are untouched.

Validation:
- The new test file: red on main (the type-argument and later-base cases
  fail, the case that a base's own method is still reached passes), green here.
  We added the Mixed and quoted forward-reference cases to the contributor's test.
- A/B against main on 7 Python repos, 670,226 edges on main: requests, flask,
  litestar, mypy, polar's server, django unchanged, sqlalchemy 1 edge removed,
  0 added, 0 retargeted. That edge is a.references(b) in relationships.py. Its
  local a named a test's class a(TypedColumns), and TypedColumns' type argument
  "Column[Any]" reached Column.references: the right method by chance, by the
  path this fixes. Its twin b.references(a) two lines down has no edge in
  either arm.
- Controls express and gin: full dumps byte-identical.
- Kernel parity on flask and requests: 43/43 in both arms (the kernel is not
  touched). Index cost on sqlalchemy, median of 3 interleaved: 29.5 s on main,
  25.7 s here, so nothing measurable.

Original PR #3000 by @JosefAschauer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 17:05:11 +00:00
Colby MchenryandClaude Opus 5.5 3f66df358e docs: add a contributing guide and a documentation index (#3081)
A new contributor had nothing to start from: the README covers using
CodeGraph, and the build and test rules live in AGENTS.md, written for
agents. CONTRIBUTING.md now covers building from source, testing a change,
preparing a pull request and what happens to it. docs/README.md indexes the
guides and design notes, and the README links to both.

Every relative link and heading anchor was checked against main.

Reimplements PR 1931 by @mixxer. Also folds in the fork-and-upstream setup,
`npm run cli`, `npm run test:watch` and the version rule from PR 306 by
@marcelovani, and the commit format, the single-test command, the bug-report
list and the `/add-lang` pointer from PR 665 by @ymstar.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 16:37:56 +00:00
Colby MchenryandClaude Opus 5.5 a0c6c1b17c fix(liquid): a variable named with a hyphen is indexed under its whole name (#3080)
Liquid allows hyphens in variable names (`{% assign form-field-label = … %}`,
`{% capture icon-cart %}`), but the extractor read assign and capture
names as \w+. PR #2814, which added capture, made such a name get no
node rather than a cut-short one, so hyphenated variables were missing
from search and codegraph_explore.

Both declarations now read a name as a word character followed by word
characters and hyphens. A capture's bare name is matched lazily up to
whitespace or the tag's end, so in `{% capture title-%}` the hyphen
still belongs to the -%} whitespace control and the name is `title`,
while `{% capture title-text-%}` reads `title-text`. A name that goes on
with a dot (`ghost.name`, `ghost-name.x`) still gets no node, in both
tags. Liquid isn't extracted by the native kernel, so there is no
kernel side.

Validation: extraction.test.ts gains 5 capture forms (bare, tight -%},
trimmed, quoted, a {% liquid %} line) and an assign test (braced,
trimmed with no spaces, a {% liquid %} line); they fail 6 of 6 with
main's extractor and pass with the fix, and the cut-short guard now
covers dotted names in both tags. A/B, each arm built from its own
checkout, on PR #2814's theme set (Shopify/dawn 05222537,
Shopify/horizon dfad90d8, Shopify/skeleton-theme a7a655e7,
ChumsInc/chums-impulse-dev 4fd6f08e, agencecinq/cinquante-et-un
ecb0035a, noclocks/shopify-devstore-theme e1747695, panoply/syncify
98d75fd0, Shopify/theme-tools bb33f49c) and controls expressjs/express
0dee2c52 and psf/requests 3c7baaa0: all ten byte-identical, as none of
them uses a hyphenated name. On three themes that do (Zoront22/LOS
58dc2dfc, lucidnz/bootstrapify-1 b36ab7ff, ibarake/bittergracedc
e36fa5db) the fix adds 4, 25 and 39 variable nodes, each with its one
contains edge: exactly the 68 hyphenated declarations a separate scan
finds, each checked to sit on a capture or assign tag naming it.
Nothing is removed or retargeted, no unresolved ref changes, and file
rows differ only in their node counts. Index time, median of six
alternating runs: horizon 3.60 vs 3.64 s, bittergracedc 28.39 vs
28.24 s.

Reimplements the part of PR #2504 by @Puma7 that PR #2814 left out.

Refs #2498

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 16:10:53 +00:00
Colby MchenryandClaude Opus 5.5 a3e9e760b1 fix(explore): Flow reaches a named symbol a shorter route gets to first (#3079)
The named walk behind codegraph_explore's Flow (and the viewer's
/api/flow) kept one route per node and replaced it only with a better
route of the same length. In entry -> mid1 -> deep -> leaf beside
entry -> mid2 -> leaf, leaf was reached first through the unnamed mid2,
so the route through the named deep was turned away for being longer,
and the query "entry deep leaf" got a Flow that dropped deep or leaf.
On django, SQLCompiler.as_sql pre_sql_setup get_select ran as_sql ->
get_qualify_sql -> get_select and left out pre_sql_setup (issue #2970).

A node now keeps every route to it that no other route to it beats: one
that got there no later, through as many named symbols, ending on no
more unnamed hops. That is the same-depth rule of PR #2453 widened, so a
longer route through more named symbols survives, while a longer route
through fewer is still turned away and can't win the deepest-sink
choice; that choice and the longest-chain ranking across seeds are
unchanged. A route that beats one waiting at its own depth takes its
place in the queue, so nodes are visited in the order they were
reached, as before. A route never passes a node twice: with several
routes per node, a cycle among named symbols (ping -> pong -> ping)
would count them again and out-rank the flow it repeats. Each node's
callees are read once per search, across seeds.

The explore-exact-target fixture's Flow now runs through every symbol
its query names, as django's does. Its compiler.py stays a per-symbol
view only while the named and spine bodies outgrow the file's share,
which django's do (18,390 chars against 8,895, measured on django/db at
11af25c0) and the miniature's no longer did once the oversized unnamed
bridge left the spine, so its get_select grows to django's proportions;
no explore render rule changes.

Validation: new flow-named-longer-route.test.ts (issue repro through
resolveNamedSymbolFlow and codegraph_explore, the bridge budget, no
cycles) and the updated explore-exact-target fixture: 3 assertions fail
with main's walk, all 11 pass with the fix; 64 other Flow tests pass.
Explore A/B, both arms on one index per repo (expressjs/express
0dee2c52, gin-gonic/gin 0f09c3a9, django/db of django 11af25c0,
excalidraw d3a9c2a1), 290 queries: 152 graph-derived #2970-shape
queries all changed their lead chain, each to one more named symbol
(37/37, 55/55, 60/60); of 125 random named-chain controls 11 changed
and of 32 hand-written flow queries 1 (django's), each gaining a named
symbol; no query lost one, no chain repeats a node, and every query
whose Flow is unchanged returns a byte-identical answer. Largest answer
24,997 -> 24,998 chars (cap 25,000). getCallees reads per query set
drop 35-50% (gin 657 -> 410, django 1207 -> 752, excalidraw
1407 -> 951); explore time unchanged within noise.

Reimplements PR #3003 by @johnhldiver-beep.

Fixes #2970

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:52:44 +00:00
Colby MchenryandClaude Opus 5.5 910e9bd86f fix(site): agent lists include GitHub Copilot, and Codex notes its IDE extension (#3066)
The site's agent lists stopped at Kiro, though the installer configures
GitHub Copilot in VS Code, the Copilot CLI and JetBrains IDEs, and the
README lists it everywhere. Copilot is now in every list: Integrations,
Installation (the detected agents and the restart line), Introduction,
Quickstart, Indexing and the landing page.

The Integrations page's Codex CLI entry now says the Codex IDE
extension reads the same config: $CODEX_HOME/config.toml (default
~/.codex/config.toml) for a global install, and .codex/config.toml,
which Codex uses only in a trusted project, for a local one, as
src/installer/targets/codex.ts writes them.

Installation said "Cursor and Kiro get the MCP config only", which,
with more agents listed, read as if every other agent gets an
instructions-file section. It now names the four that do (Claude Code,
Codex CLI, Gemini CLI and opencode); the others get the MCP config
only.

Validation: site npm ci and astro build pass (21 pages); the built
pages carry the new entries.

Reimplements the site half of #549 by @ashishpatel26.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:50:29 +00:00
Colby MchenryandClaude Opus 5.5 03c10ada87 ci(site): move the site deploy off the Node 20 action runtime (#3048)
The "Deploy site to GitHub Pages" workflow still used
actions/checkout@v4, withastro/action@v3 (setup-node v4 and
upload-pages-artifact v3 inside) and actions/deploy-pages@v4, all on
GitHub's deprecated Node 20 action runtime.

It now uses actions/checkout@v6, withastro/action@v6 and
actions/deploy-pages@v5, all on Node 24, pinned by major tag as
release.yml pins its actions. The tags resolve today to checkout v6.1.0,
withastro/action v6.1.4 and deploy-pages v5.0.1. checkout stays on v6 to
match release.yml; v7 mainly blocks fork checkouts in
pull_request_target.

Changed defaults, read from each release's notes and action.yml:
- checkout v5 and v6: Node 24 (runner 2.327.1 or newer), and persisted
  credentials go to a separate file. The breaking change in v6.1.0
  concerns only pull_request_target and workflow_run checkouts, which
  this job doesn't do.
- withastro/action v4 to v6: the node-version default went from 20 to
  24; this workflow sets 22 and keeps it. Install and build are still
  npm install and npm run build in site/. A new Astro build cache
  (node_modules/.astro, on by default) is restored before the build and
  saved after. The upload is upload-pages-artifact v5 with
  include-hidden-files: true, which packs the same files v3 did, and
  the built site has no dotfiles anyway.
- deploy-pages v5: Node 24 and polling backoff; inputs unchanged.

Nothing else changes: triggers, permissions, concurrency, the site path
and node-version 22. The YAML parses, and the site builds locally with
Node 22 (21 pages). The workflow was not run, because a run deploys the
live site.

Raised by PR 881 (@Dashsoap).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:49:09 +00:00
Josh66andClaude Opus 5.5 0d7480f83b fix(cpp): an overload chosen by arguments that call it again no longer overflows the stack
On main, indexing darts-clone failed in "Resolving refs" with "Maximum call
stack size exceeded", and the whole run was lost. darts.h writes
`extras(extras(id).prev()).set_next(extras(id).next())` on a class with a
const and a non-const `extras(id)`. Choosing between them types the
arguments; typing `extras(id).prev()` types `extras(id)`, whose overload is
chosen by the arguments of the call the reference is at, the outer one, so
the same arguments are typed again. cppArgumentType restarts
cppExpressionType's depth at 0 on each lap, so the depth bound never trips.

cppArgumentTypeChoice now keeps the calls whose arguments it is typing
(`file:line:column:name`), and a choice that comes back to the same call
takes the first tied overload, the answer it already gives when no
argument's type is known. A try/finally clears the entry.

Validation on main 5526e33d (Windows 11):
- Red/green: the new test fails with main's name-matcher.ts (RangeError:
  Maximum call stack size exceeded) and passes with the fix.
- A/B against main: darts-clone fails on main and indexes with the fix,
  503 more linked sites (897 edges against the 394 the failed run left),
  with `reserve_id` and `expand_units` reaching `extras`, `prev`, `next`,
  `set_prev` and `set_next`. leveldb, fmt, googletest and nlohmann/json are
  byte-identical, as are the express and flask controls.
- Index time unchanged: median of 3 interleaved runs on nlohmann/json,
  15.9 s on main and 16.0 s with the fix.

Original PR #2999 by @JosefAschauer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:41:11 +00:00
Colby MchenryandClaude Opus 5.5 fa03fa6bb4 fix(callers): list every call site of a caller, and a function that calls itself (#3077)
getCallers keeps one row per caller (issue #1086) with the caller's first
edge only, and seeds its reported set with the symbol itself, so
codegraph callers showed a caller that calls the symbol on two lines
once, at the line its own declaration starts on, and left a recursive
call out, though the index stores every one of those edges and each is
a line to edit when the symbol changes. The CLI also merged edges on
source, target and kind, which dropped a second call site from --json.

A new GraphTraverser.getCallSites (CodeGraph.getCallSites) reads the
direct callers or callees with every edge: one row per neighbour in the
order getCallers / getCallees list them, every site kept, and the
symbol's own row, flagged recursive, when it calls itself. getCallers
and getCallees are unchanged, so ranking, explore's Flow and blast
radius, impact and the viewer read exactly as before; a test pins that
every non-recursive row of getCallSites equals getCallers' row and first
edge. src/graph/call-sites.ts holds the one wording of a site list
(9, 10, +N more) the surfaces share.

- codegraph callers prints a caller at its call-site lines (up to 10,
  then +N more), a recursive row as "(calls itself)", and --json gives
  each row lines and recursive, with every site in edges. Callees keep
  the callee's declaration line, where a call leads.
- codegraph_callers / codegraph_callees read the same rows (10 sites per
  caller), and codegraph_node's trail shows callers at their sites, 3 at
  most, and the symbol once among its callers when it calls itself.

Validation: new callers-call-sites.test.ts (7 tests) fails 7 of 7 with
main's sources and passes with the fix; 11 neighbouring callers, trail
and lookup test files (217 tests) pass. Before/after on one index per
repo (expressjs/express 0dee2c52, excalidraw d3a9c2a1, gin-gonic/gin
0f09c3a9): trails changed for 108/253, 3630/4180 and 557/1395 symbols,
nearly all callers moving from the declaration line to the call sites;
recursive rows newly shown 2/20/7. Budget: trail median 115->117,
354->360, 185->187 chars, largest growth +131/+212/+91 chars, and the
busiest caller rows (67, 300 and 100 sites) stay one capped entry.
codegraph_callers on each repo's 15 busiest callees: largest answer
1025->1358, 1882->2127, 1790->1805 chars.

Not in this change: the issue's own recursion, child.walk() on a
for...of element over children: TreeNode[], is not linked at all on
main (the receiver's element type isn't inferred), so it needs a
resolution fix of its own; this.walk() and a plain recursive call are.

Reimplements PR #2994 by @johnhldiver-beep.

Fixes #2909

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:30:39 +00:00
Eric MinishandClaude Opus 5.5 59eb0d2820 fix(resolution): an import no longer lands on a same-named method of an exported object
An exported object literal's methods (`export const d = { f() {} }`) are
indexed as exported nodes named `f` (qualified name `d::f`), and the
per-file export index kept the first exported node per name. So
`import { f } from './m'` could link to `d.f` instead of the module's own
`export function f`, and which one won depended only on declaration order.

A JS/TS member, a node whose qualified name differs from its name, now
ranks behind the module's own bindings wherever an import is matched to an
export: a named import (the module's own `f`, then its export clause, then
its re-exports, then a member), an export clause's local name,
`export default f` and `module.exports = f`. A member is never dropped:
`export const { f } = d` binds `f` with no node of its own, and `d::f` is
its only answer. The default-import guess no longer picks a member.

Validation on main de0a4eb3 (Windows 11):
- Red/green: 7 of the 13 new tests fail with main's import-resolver.ts;
  all 13 pass with the fix, with the kernel and with CODEGRAPH_KERNEL=0.
- A/B against main: express, vuejs/core and excalidraw are byte-identical,
  as are the flask and gin controls. codegraph's own source retargets 195
  sites, each from a `hashNavigation` method to the exported function of
  the same name in ui/src/lib/navigation.ts, the issue's case. vscode's
  base and editor retarget 328 sites: 321 imports and calls of `join`,
  `basename`, `dirname` and 5 other path functions move from the `win32`
  object's methods to path.ts's own exports
  (`export const join = (platformIsWin32 ? win32.join : posix.join)`), and
  7 `marked.lexer` and `marked.parse` calls move from a `_Tokenizer` field
  and a `_Parser` static method to the `lexer` and `parse` that marked.js
  exports. No edge is added or removed.
- Index time unchanged: median of 3 interleaved runs on vscode's base and
  editor, 16.6 s on main and 17.2 s with the fix.

Original PR #2990 by @inth3shadows.
Fixes #2945

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:20:22 +00:00
Max HsuandClaude Opus 5.5 1c40e34141 fix(mcp): a projectPath naming a file resolves through its directory
An agent that passed the file it was looking at as `projectPath` got
`isError: true` ("Path is not a directory"), while a path that doesn't
exist at all walked up to the project's `.codegraph/` fine. An error teaches
an agent to stop calling codegraph, and this mistake is recoverable.

`execute()` now takes an existing file to stand for its directory, right
after the length check, and rewrites `args.projectPath` there, so the
project gate, the worker dispatch, the worktree notice and getCodeGraph all
see that directory. A path that can't be stat'd walks up as before.

Path safety: the directory goes through the same checks as any
projectPath, the sensitive-folder refusal on the path itself and on the
root its up-walk lands on, so a file reaches exactly what its directory
reaches and never more. `/etc/hosts` is refused as `/etc` is, a file in
`~/.ssh` as `~/.ssh` is, and `win.ini` in the Windows folder as that folder
is. A symlink inside a project that points at a file in a sensitive folder
is answered from the link's own folder, as a symlinked folder already is;
nothing in the sensitive folder is opened.

Validation on main de0a4eb3 (Windows 11):
- Red/green: the PR's 2 tests (a file in an indexed project, and a file in
  a linked worktree, which keeps its worktree notice) and 1 of ours fail
  with main's tools.ts and pass with the fix. Ours asks for a file and for
  its directory in 4 cases, an indexed project, `~/.ssh`, a folder in no
  project, and the Windows folder's `win.ini`, and requires the same
  answer for both, refusals included.
- A real `serve --mcp` session over stdio with a private HOME: on main,
  codegraph_search and codegraph_status for `<project>/src/a.ts` both
  returned isError "Path is not a directory"; with the fix both answer from
  the project, and `win.ini` is refused as a sensitive system directory.

Original PR #2996 by @maxmilian.
Fixes #2982

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 15:00:53 +00:00
Eric MinishandClaude Opus 5.5 5526e33d1d fix(status): recommend a re-index when package.json alone adds or drops a framework
Since PR #2941, a sync records the frameworks that came or went since the
last full index, and `codegraph status` recommends a re-index. But a sync
detects frameworks again only when it extracts a file, so adding `express`
or `@sveltejs/kit` to package.json with no source file edited recorded
nothing: status said the index was up to date while an unchanged Express
app's routes, or the `goto('/login')` in an unchanged +layout.svelte,
stayed unlinked until a full index.

A full index now also stamps the resolver's framework set, and
getFrameworkChangesSinceIndex() adds the difference between that stamp and
the set the resolver detects now (it detects on every open) to what syncs
recorded. So a fresh `codegraph status` sees a manifest-only change whether
or not a sync ran. An index built before this has no stamp, so that half
starts at its next full index. A long-running server's resolver keeps its
old set until it extracts a file, as before.

Validation on main 61776927 (Windows 11):
- Red/green: 3 of the 4 new tests fail with main's src/index.ts; the 4th,
  an unchanged project staying silent, passes on both. All 4 pass with the
  fix, as do the 8 sync-framework-detection tests.
- The CLI before and after, on a SvelteKit fixture indexed without
  @sveltejs/kit, then given it in package.json, then synced: main's status
  says "Index is up to date", and --json has reindexRecommended false and
  frameworksChangedSinceIndex null. With the fix, status adds "Frameworks
  changed since the last full index (added sveltekit-router)", and --json
  has true and {added: [sveltekit-router]}. Dropping the dependency gives
  {removed: [sveltekit-router]}, adding express to an Express app gives
  {added: [express]}, an unchanged project gives null on both arms, and a
  full `codegraph index` clears the advice.
- No false advice: a fresh index and then `status --json` on 18 real repos
  reports no change on any. They include express, flask, gin, vuejs/core,
  excalidraw, vuejs/docs, starlight, codegraph's own source and vscode's
  base and editor; Express, Flask, Next.js, React, Vue, Vue Router, Astro,
  Svelte, Spring, Go and UIKit are detected among them.

Original PR #3005 by @inth3shadows.
Fixes #3007

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 14:36:12 +00:00
Colby MchenryandClaude Opus 5.5 063708ba53 fix(pascal): Delphi chained calls and method pointers follow declared types (#3065)
Four Delphi bugs that PR 2550 by @OleksiyPenkov found, reimplemented on
main's Pascal scope code rather than as a second resolver:

- A call through a chain of members and methods recorded only the outer
  method's bare name, which name matching gave to any namesake: SynEdit's
  Canvas.Font.Assign(Font) went to TProposalColumn::Assign, and
  TLogger2.Create.Write('y') linked nothing, a bare Write being a System
  name. The extractor now writes such a call as the typed chain
  pascal-scope already resolves for paren-less names ({call} for a
  statement, a new {args} mode for a last link written with its
  arguments). Each link is typed by its declaration: field and property
  types, function results, a local's declared type, through pointer and
  class reference types (PVirtualNode = ^TVirtualNode, TSynLogClass =
  class of TSynLog) and explicit dereferences (a^.Copy). A constructor
  called on a class gives an instance of it, a unit name, dotted ones
  too, qualifies its declarations, and a chain called with arguments may
  end at data that holds a routine. There is no bare fallback: a chain
  through a type from outside the project links nothing, and in a with
  body only a chain from Self or a typed local is read.
- A method given to a target was a method pointer only when the target
  was named On.../FOn...: Callback := FProvider.Value with Callback: TGet
  recorded a call, and FOnGet := @FProvider.Value nothing. A value given
  to an assignment now carries its target, whose declared type decides
  (routine types written out, of object, reference to, project aliases,
  the RTL's routine type names; a class, a record or a System value type
  holds no routine); the name decides only where the declaration can't
  be read. A function that returns a routine type is called for it, and
  @Obj.Method is a reference anywhere.
- A nested routine's locals leaked into the routine around it: the name
  matcher's Pascal receiver scan read every declaration above the call.
  It now steps over routines nested elsewhere, reads the calling
  routine's own name lists (Doc, Doc2: TDocVariantData), which main typed
  only by luck through a nested routine's parameter, and follows pointer
  and class reference types. Where the tree has errors, the source-text
  scopes give the outer routine its own names back after a nested one.
- A nested routine declared forward is in scope from that declaration.

Validation:
- New __tests__/pascal-reference-boundaries.test.ts, 41 tests, 24 of
  them ported from PR 2550: 22 fail on main's sources, the other 19 pin
  what main already got right. pascal-chained-calls and pascal-for-in-var
  pinned the bare outer-method names and now expect the typed chains
  (4 tests, failing on main). Twenty mutations, one per rule, each fail
  a test.
- A/B against main 80f6b505, both arms built from their own sources and
  diffed by natural keys, edges removed/added: SynEdit 195/66, HeidiSQL
  789/320, mORMot2 2553/4164, DelphiMVCFramework 2394/1850, DWScript
  without its Test folder of scripts (519 files) 864/801. leveldb and
  SDWebImage byte-identical.
- Removed edges, hand-triaged: SynEdit all 195, 193 namesakes or parse
  artifacts and 2 right ones lost (Get(i).LoadFromStream in a with
  body); samples of HeidiSQL 20/20, DelphiMVCFramework 30/30, DWScript
  12/12 and mORMot2 23/25 namesakes (of the other two, one now links the
  unit's own CompareMem, and one right edge is lost, through a field
  declared after the first name of a name list, which the extractor
  gives no node).
- Added edges sampled right: typed chains 186 of 187 (the wrong one
  reaches the FMX variant of a conditional ancestor), receiver calls
  40/40, method pointers, @-references and kind changes 57/57.
- CPU, median of 3 interleaved: SynEdit +6.6%, HeidiSQL +0.6%, mORMot2
  -2.5%, DWScript +4.7%, while the identical controls moved 0.0% and
  -5.9%. DelphiMVCFramework, timed before the scan's memo was split per
  routine (which only made it cheaper): -6.6%.

Reimplements part of PR 2550 by @OleksiyPenkov.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 14:29:03 +00:00
Colby MchenryandClaude Opus 5.5 fd57eaaa45 fix(mcp): a tools/call whose arguments aren't an object gets invalid params, not a crash (#3071)
A tools/call request passes its arguments as an object. MCPSession took
params.arguments || {} without checking that, so a string or number went
straight to the tool handler, where the session-view check
('_cgExploreSession' in args) threw. The call then came back as a tool
result flagged isError: "This is an internal codegraph error, retry the
call once; if it persists, continue without codegraph". That reports a
client's malformed request as codegraph's own malfunction, with advice to
stop using it. An array went through as if it were the arguments. The
stdio proxy, serving in process while the daemon is unavailable, had the
same unchecked read.

Both now read the arguments through one helper, toolCallArguments(), and
answer anything but an object with a JSON-RPC invalid-params error
(-32602, "Tool arguments must be an object"), as a call with no tool
name already is; no tool runs, and the proxy starts no engine for it.
Missing, null or another empty value still means no arguments.

Validation: new mcp-tool-call-arguments.test.ts covers the session (the
direct stdio server and every daemon client) and the real proxy entry
point in a child process with the daemon unavailable: red on main (2 of
3 failed; the well-formed control passed), green with the fix.
explore-session-state and proxy-shutdown pass. Driving serve --mcp over
stdio: on main, codegraph_explore, codegraph_node and codegraph_search
with a string argument returned isError "internal codegraph error" and
codegraph_status accepted [1], 42 and true; with the fix those six get
-32602, while "", null, {} and absent arguments run as before.

Reimplements PR #2986 by @kjgggggg.

Fixes #2981

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 14:16:43 +00:00
Colby MchenryandClaude Opus 5.5 de0a4eb362 fix(vue): a self-closing <script /> no longer swallows the next script (#3070)
The Vue extractor read a self-closing `<script src="./legacy.js" />` block
as an opening tag running on to the next `</script>`, as the Astro and
Svelte extractors did until PR #3063 (PRs #2995 and #2997) landed. The
`<script setup>` after it was parsed with whatever lay in between and
contributed nothing, and a `<template>` in between lost its calls and its
components too. One copy of the same pattern sat in each of 9 places in 5
files, and that fix reached the 6 copies in Astro, Svelte and the viewer.

sfc-script.ts, which the Vue, Svelte and Astro extractors already share,
now exports the script pattern and the script-or-style pattern, built from
@maxmilian's regexes, plus sfcBlockLineRanges, the line ranges a template
scan skips. A self-closing tag has no body, so it covers nothing and isn't
blanked, and calls in its attributes are read. All 9 sites use them: each
extractor's script blocks, Astro's covered ranges, both Svelte template
scans, Vue's template-components scan, the Vue template-calls blanking
and the viewer's highlight regions. The pair also accepts a closing tag
written with a space, `</script >`, as the template-calls blanking always
did; the viewer finds a block's body from its opening tag for that reason.

Validation on main 61776927 (Windows 11):
- Red/green: 4 Vue tests (a `<script src ... />` block before
  `<script setup>`, one before `<template>`, an attribute call on a
  self-closing script in the template, and `</script >`) fail with the
  previous sources and pass; the 6 Astro and Svelte tests still pass.
- A/B: 5 Vue repos (vuejs/core, vuejs/docs, NekoBox, justgage,
  element-plus-playground; none has a self-closing script) are
  byte-identical to main. 7 Astro repos, 2 Svelte subtrees (shadcn-svelte
  docs routes, SvelteKit's basics test app) and the flask and express
  controls are byte-identical to the Astro and Svelte fix before this one.

Fixes #2989

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 14:02:53 +00:00
Colby MchenryandClaude Opus 5.5 cb7fb61e76 fix(docs): agent and command lists match the code; worktree warning drops init -i (#3067)
The warning for a git worktree answered from another checkout's index
still said to run "codegraph init -i", a flag that has done nothing
since init started indexing by default. Its one-line form is prepended
to every read-tool result and codegraph_status embeds the long form, so
both told the agent to build the index, which the server instructions
rule out ("Indexing is the user's decision ... don't run it yourself").
The CLI's codegraph status now says: Run "codegraph init" in this
worktree. What an agent reads (the read-tool notice, which also reaches
it through the prompt hook and the explore/node CLI, and
codegraph_status) says the user can run "codegraph init" there.

Docs that no longer matched the code:
- AGENTS.md listed 4 of the 11 installer targets, called a new one "a
  5th agent", said the contract suite covers "all 4" targets, and listed
  11 of the 24 subcommands. It now lists every target and subcommand,
  and names the hidden ones (serve --mcp, prompt-hook, and ui/web unless
  CODEGRAPH_UI=1).
- README's Supported Agents section said no instructions file is
  written, but Claude Code, Codex CLI, Gemini CLI and opencode get the
  short CodeGraph section. Its Codex entry now says the Codex IDE
  extension reads the same config: $CODEX_HOME/config.toml (default
  ~/.codex/config.toml) for a global install, and .codex/config.toml,
  used only in a trusted project, for a local one.
- README's WSL2 "Transport closed" entry named only the in-process
  fallback. The daemon also moves its socket to the temp directory when
  the project's filesystem can't host one.
- init -i and -iv leftovers in internal docs, scripts, the add-lang
  skill and the repo's own Cursor rule, which now also leaves indexing
  to the user. Two stay on purpose: scripts/agent-eval/audit.sh can
  audit a published version older than 0.9.8, where init built the
  index only with -i (now commented there), and
  docs/benchmarks/codegraph-ab-matrix.md records a 0.9.4 run.

Validation:
- worktree-detection.test.ts: on main 61776927's worktree.ts and
  tools.ts, 4 of its 20 tests fail (the CLI wording, the agent wording,
  the read-tool notice and codegraph_status). With only the worktree.ts
  fix, the codegraph_status test still fails. All 20 pass here, and so
  do mcp-nested-repo-projectpath.test.ts's 13.
- Full suite on this patch over 61776927 (CODEGRAPH_KERNEL_EXPECT=1,
  4 workers): 815 files (809 passed, 6 skipped), 9608 tests passed,
  0 failed, 86 skipped.
- Rebased unchanged onto f67eafcb. Its three new commits share only
  CHANGELOG.md with this PR, in other bullets. On the rebased tree these
  pass (81 tests): worktree-detection, mcp-nested-repo-projectpath, and
  the new commits' default-export-declaration,
  rust-path-attribute-modules, rust-path-super-glob,
  search-special-characters and strip-comments.

Reimplements #549 by @ashishpatel26, #651 by @GaoSSR, #885 and #886 by @Dashsoap, and #1083 by @zengwenliang416.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 13:47:59 +00:00
Colby MchenryandClaude Opus 5.5 f67eafcbc5 fix(search): a pasted call like leaf(entry) finds both names instead of nothing (#3069)
Full-text search dropped the FTS5 syntax characters ( ) ^ " ' * : from a
query before quoting each word, so the words on either side of one were
glued together: leaf(entry) became the single prefix term "leafentry"*,
which no symbol has, and the LIKE and fuzzy fallbacks don't recover it.
codegraph query, the codegraph_search tool and searchNodes() all came
back empty for a pasted call like render(props).

The index's unicode61 tokenizer splits stored text at anything but
letters and digits (a signature's leaf(entry) is stored as leaf and
entry), so the query now splits there too: each of those characters
becomes a space, the treatment :: already gets (issue #173).

Validation: new search-special-characters.test.ts (8 tests) fails 8 of 8
on main and passes with the fix; fts5-fallback, search-field-filters,
search-query-parser, cli-query-command and symbol-lookup pass. A query
A/B on expressjs/express 0dee2c52, both arms over one index: 12 control
queries without such a character between words are byte-identical; 10
pasted calls changed, 7 of them from no results to results led by the
function they name (res.send(body), res.json(obj),
View.prototype.lookup(name)).

Reimplements PR #2987 by @kjgggggg.

Fixes #2971

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 13:31:02 +00:00
Colby MchenryandClaude Opus 5.5 cc17978174 fix(rust): a module a #[path] attribute loads is the module that declares it (#3064)
A Rust module loaded with `#[path = "…"]` was found by its file's directory:
fast-mlsirm's `#[path = "../../../tests/unit/scaling_tests.rs"] mod tests;`
in `crates/core/src/scaling.rs` made `tests/unit/scaling_tests.rs`'s
`use super::*` walk to a `tests/unit` module that doesn't exist, so its
`predict_rating_multi(1)` linked to nothing, or to a same-named function of
another crate; its `crate::` had no crate, and the parent's private items
looked out of its reach. From the declaring side, a path through such a
module (`utils::mock_event(…)` under `#[path = "./utils.rs"] mod utils;`)
reached nothing.

The fix reads each file's `#[path]` declarations as the Rust Reference
reads the attribute (from the declaring file's directory, or inside an
inline `mod` from that module's own; a path that leaves the project, by
escapesRoot, or that a `cfg_attr` sets, names no file):
- rustSubmodule: a module the module declares once with a `#[path]` is
  the file it names, whatever else loads that file too (a helper several
  tests load is each test's); cfg alternatives that name a file each stay
  unknown, and a path's 2015 crate-root fallback no longer reaches past
  such a module to a namesake at the crate root.
- rustPathClaim: a file the regular rules don't place is the module of the
  one `#[path]` declaration that loads it, if exactly one does. Placed
  (rustPlacedByName) are crate roots, files with a `fn main` or
  `#![no_main]` of their own (trybuild cases, fuzz targets), and files a
  plain `mod name;` declares in the module owning their directory or in an
  inline module of one above it (dioxus's `mod components { pub mod home; }`
  in main.rs). Only for a file left over are the project's Rust files that
  write `path =` read (a byte check first), once per resolver. With a
  claim, rustSuperModule is the declaring module, rustFileModule owns the
  file's directory (rustc reads every `#[path]` file as a mod.rs),
  rustCrateRootModule is the declaring file's crate, and rustModuleWithin,
  isRustItemVisibleFrom and isVisibleAcrossFiles see the file inside the
  declaring module, so `use super::*` brings in its private items.
- rustCrateGraph: `[[example]]`, `[[test]]` and `[[bench]]` paths are
  target roots, as `[lib]`/`[[bin]]` ones are since PR #3014, and such an
  example is its own crate's root (dioxus's
  `examples/07-fullstack/handling_errors.rs`).

Validation:
- rust-path-super-glob.test.ts (PR 1892's case, credited) and
  rust-path-attribute-modules.test.ts (7 cases): on main all 8 fail; all
  pass. Every rust-* suite passes.
- A/B against main, native kernel: fast-mlsirm (its Rust files) +2,796
  links (1,839 calls, 427 references, 334 constructions, 196 imports), 71
  retargeted (exposure_tests.rs's `Lcg::next_f64` from cdm_tests.rs's
  private `Lcg` to exposure.rs's, the declaring module's helpers instead
  of bifactor_grm.rs's), 87 reaching the same item through the declaring
  module (confidence 0.4 to 0.9), 0 removed; dioxus +27 (each headless
  test's `utils::mock_event(…)` into the helper five tests load); tokio +2
  (`use super::AtomicU64` in the files atomic_u64_as_mutex.rs loads);
  ripgrep, axum, clap, serde, gleam, express and flask unchanged.
- Cost, native kernel, medians of 3 interleaved runs: fast-mlsirm CPU 15.3
  -> 15.8 s, wall 4.2 -> 5.2 s, peak RSS 825 -> 882 MB; tokio CPU 26.1 ->
  26.7 s, wall 10.4 -> 11.2 s, peak RSS 1,023 -> 1,028 MB; dioxus CPU 34.8
  -> 35.6 s, wall 10.3 -> 11.2 s, peak RSS 1,125 -> 1,120 MB; gleam CPU
  24.1 -> 23.8 s, wall 6.6 -> 6.7 s, peak RSS 1,027 -> 1,023 MB.

Builds on PR #1892 by @seonghobae.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 13:21:12 +00:00
Colby MchenryandClaude Opus 5.5 ed6b88e53a fix(js): an export default line inside a template literal no longer names the default (#3068)
statedDefaultExport reads a JS/TS file's own export default statement
by scanning comment-stripped source for line-initial `export default`
heads. Strings are deliberately not masked there (a masker that loses
step on nested templates blanked real statements), and a head counted
when it named a node of the file, the first such head winning. A code
generator's template text breaks that: in

  export function App() {}  export function Main() {}
  export const template = `
  export default App
  `;
  export default Main;

the template's line names the real App, so `import X from './gen'`
bound to App instead of Main (issue #2968). A template holding
`export default () => …` also made a module whose real default is an
expression read as anonymous, which keeps every guess away.

templateLiteralTextAt (strip-comments.ts) scans the source once for
template-literal text: it follows `${…}` nesting (a template inside an
interpolation, a brace inside a regex there), and skips comments,
quoted strings and regex literals, which may hold a backtick; a `/`
after a value divides, anywhere else it opens a regex. A head inside
template text is now skipped. When some template never closes the scan
vouches for nothing and every head counts, as before. Nothing else
changes: a head outside template text is read exactly as it was.

Validation: default-export-declaration.test.ts gains the issue's file,
a template returned by a function behind a nested template, one passed
at module scope and one in a class field, a template's anonymous
default above an expression default, and controls (a regex and a string
holding a backtick, a division after a parenthesis, and a file whose
scan can't close a template); strip-comments.test.ts tests the scan
directly. Red with main's resolver: 2 of 10 failed; green: all pass.
Checked against tree-sitter on every line-initial head of 4,191
JS/TS files in 16 corpora (outline, excalidraw, vben, bitwarden apps,
mastodon, shadcn docs, zod, bulletproof-react, express, astro, react,
trezor-suite, this repo's src, tests and ui): of 4,149 real export
default statements the scan puts none inside template text, and all
322 heads it does place there are template text. A/B on excalidraw
d3a9c2a1, vben 61c07936, astro e3bec3d2 (packages/astro/src and
packages/integrations), with gin-gonic/gin 0f09c3a9 and psf/requests
3c7baaa0 as controls, both arms on main 4b0f72b7 through the native
kernel (and again on 66449255 through wasm): all six byte-identical,
since no default import there is decided by template text; index time
unchanged.

Not in this change: hasEsmDefaultExport, which only gates
require('./x').default, still reads the raw text.

Reimplements PR #3042 by @johnhldiver-beep.

Fixes #2968

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 12:55:21 +00:00
Max HsuandClaude Opus 5.5 617769279d fix(astro,svelte): a self-closing <script /> no longer swallows the next script
A self-closing `<script ... />`, such as Astro's
`<script is:inline set:html={code} />` or a third-party
`<script src="/analytics.js" />` in Svelte's `<svelte:head>`, matched the
extractors' script regex as an opening tag, so the match ran on to the next
`</script>`. The real script that followed was parsed with the markup in
between, failed with "parse produced no symbols", and contributed nothing.
The covered-range regexes had the same shape, so the template scans also
skipped the markup between the two tags, and a self-closing `<style />` hid
the markup after it.

The opening-tag pattern now matches a `/>` ending on its own as an empty
tag: in the Astro extractor's script blocks and covered ranges, the Svelte
extractor's script blocks and both of its covered-range scans, and the
viewer's highlight regions.

With a fix of ours: a self-closing tag has no body, so the covered-range
scans skip it, and a call in its attributes, like
`set:html={serializeJsonLd(schema)}`, is read as on main. Matched as a
range, such a tag hid those calls even where no script followed it.

Validation on main bc9291af (Windows 11):
- Red/green, 6 tests: 4 from the PRs, plus 2 of ours for an attribute call
  on a self-closing script in Astro and in Svelte. With main's
  astro-extractor.ts, svelte-extractor.ts and syntax-tokens.ts all 6 fail;
  with the PRs' code as written the 2 of ours fail; with this commit all 6
  pass.
- Svelte 5.56.10's own compiler reads the Svelte fixture as an empty head
  script plus an instance script, as the extractor now does.
- A/B against main on 7 Astro repos, with flask and express as controls.
  starlight, diploi.com and both controls are byte-identical, and
  devfest-website keeps every edge. Gains: the genkit docsite 2 import
  links, nodejsdesignpatterns.com 2 nodes and 2 import links, a portfolio
  25 component references, and wm-project-astro-components 3
  `serializeJsonLd` calls from JSON-LD scripts plus 1 call in a script main
  swallowed. That repo also drops 31 false calls, CSS like
  `border-radius: var(...)` that main read as calls after parsing a
  swallowed `<style>` block as TypeScript. No other edge changes.
- Index time unchanged: median of 3 interleaved runs on
  wm-project-astro-components, 4.67 s on main and 4.52 s with the fix.

Vue's extractor has the same pattern and the same bug; a follow-up shares
one pattern across the three extractors.

Original PRs #2995 and #2997 by @maxmilian.
Refs #2989

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 12:24:40 +00:00
Eric MinishandClaude Opus 5.5 4b0f72b7a7 fix(sync): a skipped file that now indexes re-links its importers
A file over the source-size limit, or one whose parse failed, is tracked
with no nodes and its error recorded, so the imports of it fail. When an
edit lets it be indexed, sync stored it as a modified file, and only an
added file is looked up by what it can be imported as: an unchanged
importer's import of the file itself stayed failed, and so did what a
barrel passes on from it, until a full re-index. Named imports and calls
bound, since they wait by name.

A re-indexed file whose stored row had no nodes and recorded errors now
joins addedFilePaths once the store gives it nodes, so the added-file
retries and the importer and barrel walks run for it. It still counts as
modified. Deciding after the store leaves a file that changes but stays
over the limit, or still fails, alone, so it does not re-run those
retries on every sync.

Review changes: a test for the barrel shape, the one behind most of the
real-repo divergence below, and the CHANGELOG entry beside the one for
files saved with no symbols.

Validation: 5 tests; on main's source 4 fail and the stays-over-the-limit
control passes. 9 fixture edits, each compared with a fresh index of the
same tree, in a later process and in the same process: main diverged in 7
of each, this in 1, a barrel growing over the limit, where only the
edges' resolvedBy differs (same targets), as the PR noted. excalidraw with
packages/math/src/point.ts over the limit at index time and put back:
main was 1,506 edges short of a fresh index, identical here over nodes,
edges, refs and files.

Original PR #3022 by @inth3shadows.
Fixes #3016

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 12:11:35 +00:00
Eric MinishandClaude Opus 5.5 2d98c1b69a fix(sync): a call left with one candidate links after a delete or a rename
x.go() with go in two classes stays unlinked while both exist. A sync that
deleted one of them, or renamed it away, never retried that call: the
failed-reference retry looks refs up by the names the changed files carry
now, which a deleted file or a renamed-away name no longer has, and a sync
that only deletes files skips the retry. Failed refs under the names a
sync's definitionDelta lost or gained now go back to pending for the
sweep, next to the CG-33 rebind that does the same for resolved edges,
under the same per-name ceiling. CODEGRAPH_NO_REBIND=1 turns both off.

Review changes: the CHANGELOG entry beside the sync entries for calls,
with credit.

Validation: 6 tests; on main's source the 4 delete and rename tests fail
and the 2 still-ambiguous controls pass. 10 fixture edits (Python,
TypeScript, JavaScript, Go, Java), each compared with a fresh index of the
same tree, in a later process and in the same process: main diverged in 6
of each, this in none. excalidraw with excalidraw-app/data/LocalData.ts
deleted (its `save` was one of two): main was 38 edges short of a fresh
index, identical here over nodes, edges, refs and files; renaming
BinaryHeap's `pop` away re-opens 28 refs that fail again, as in a fresh
index.

Original PR #3004 by @inth3shadows.
Fixes #3006

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 12:00:19 +00:00
Colby MchenryandClaude Opus 5.5 e431491972 fix(mcp): a session whose host stops reading its output shuts down cleanly (#3060)
Issue #2991: a host can stop reading an MCP stdio server's output while
it keeps the server's stdin open and stays alive. The next response the
server wrote then failed (EPIPE), and with no listener on stdout Node
handed the error to the last-resort fatal handler, which exits 1 at
once. That skipped the shutdown that stops the engine, releases the
writer lock and waits for query workers still starting, which on
Windows can crash a process that exits under them. Stdin, the host's
PID and the liveness watchdog all still look healthy, so nothing else
noticed.

A new treatStdoutFailureAsShutdown, the twin of the stdin teardown from
issue #799, routes a stdout 'error' (and the 'close' after it) into the
owner's own shutdown, at most once, destroys stdout so later writes are
dropped, and keeps its listener so a write queued before the failure
cannot escape during the shutdown. Backpressure is left alone. It is
wired into the direct-mode transport and into the local-handshake proxy,
whose shutdown closes only this session's daemon connection and stops
the engines it owns. The legacy socket proxy (runProxy) has had no
caller since PR #580 and is left as it is.

Validation: __tests__/mcp-stdout-failure.test.ts runs a real
direct-mode serve --mcp, and the local proxy with an in-process engine
and with a stand-in shared daemon. After the test destroys its end of
stdout and sends one more request, main exits 1 in all three, the
server with "Uncaught exception: Error: EPIPE"; with the fix all three
exit 0, the server's writer.pid is released, the proxy's engine stop
runs, and the daemon closes only the proxy's connection and still
answers its other client. __tests__/stdout-teardown.test.ts covers the
guard itself. proxy-shutdown, stdin-teardown and mcp-initialize pass.

Fixes #2991

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 11:48:05 +00:00
danusha2345andClaude Fable 5.1 664492551d fix(sync): a barrel whose re-export points elsewhere re-links its importers
`c.ts` imports `foo` through `index.ts`, which re-exports it from `a.ts`.
Change the clause to `./b` and sync, and `bar` kept calling `a.ts:foo`
where a fresh index gives `b.ts:foo`. The barrel declares nothing of
`foo`, so the definition delta has nothing to rebind; no file was added
for the walks below a barrel or the added-files pass; the binding never
failed, so the retries never see it; and the name-matched-import pass
reads only bindings a name match took. `export *` moved the same way, and
a scoped sync of the barrel alone too.

The orchestrator now reports the modified ES modules whose `export … from`
statements changed, read off their import nodes (named by the module, with
the statement as signature) before and after the store. Their importers'
bindings through them go back for the sweep, up through the modules that
pass them on in turn, with the failures parked under them and the edges
into the members of what the bindings pointed at (`w.run()` with
`w: Widget`). It is the importer walk the removed-files pass uses, run
after the name-matched-import pass.

Review changes: the trigger compares the `export … from` statements
themselves. The original compared the modules a file imports and counted a
module that lost any import, so dropping a plain import from excalidraw's
`types.ts` (218 importers, no re-exports) re-opened 2,186 refs for the same
graph; it now re-opens none. Comparing statements also catches a name
dropped from a clause whose module stays (`export { foo, qux } from './a'`
to `export { foo } from './a'`), which the module set missed. Plus tests
for both, and the doc comments the new code sat between moved back.

Validation: 9 tests; on main's source 7 fail (the 2 controls pass), and
on the original trigger the 2 new ones fail. 15 fixture edits, each
compared with a fresh index, in a later process and in the same process:
main diverged in 8 of each, this in none. excalidraw with
`export * from "./utils"` in its math barrel (116 importers) retargeted to
`./constants`: main was 224 edges off, identical here over nodes, edges,
refs and files. Fresh indexes are identical to main's.

Original PR #2985 by @danusha2345.
Fixes #2978

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 11:29:45 +00:00
Colby MchenryandClaude Opus 5.5 d139865f9f fix(db): processes opening an index that needs a migration all open it (#3058)
Issue #2980: opening an index whose schema is behind read its version,
then ran each pending migration in a deferred transaction. When several
processes opened it at the same moment, those that read the version
just before another one migrated applied the same migration again, and
their open failed: on this Windows machine with "UNIQUE constraint
failed: schema_versions.version", since the version was already
recorded, and in the report with SQLITE_BUSY, which a deferred
transaction that has already read gets at once when it comes to write.

Each migration now runs in a transaction that takes the write lock up
front (BEGIN IMMEDIATE, a new option of the adapter's transaction()),
so a process that finds another one migrating waits it out on
busy_timeout, and reads the version again inside it, skipping a
migration already applied. The version the caller read stays a floor,
as before: a database built from schema.sql records only v1 and the
current version, and tests replay migrations above a version they
rewound to. An open of a current index takes no lock and waits for
nothing, as before.

Validation: __tests__/migration-concurrent-opens.test.ts. A second
process holds the write lock with version 16 recorded but uncommitted,
so the open reads 15: main fails with the UNIQUE error after waiting
1.1 s; the fix waits, opens and leaves the migration to the other
process. Three processes released at once from a stdin barrier on an
index with 150k unresolved references: main fails in round 0, the fix
opens all three in both rounds. On excalidraw's real index, 8 rounds of
three openers: main 7 rounds with failures, the fix 0. The single
process and the current-index cases pass on both.

Fixes #2980

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 11:15:26 +00:00
danusha2345andClaude Fable 5.1 80f6b50504 fix(sync): a tsconfig, jsconfig or go.mod change re-resolves the imports it governs
The resolver read tsconfig / jsconfig `paths` and `baseUrl` and go.mod's
module path once and kept the maps for its lifetime ("callers re-create the
resolver if config changes", which none did), and the watcher follows source
files only. So after an edit to one of them a long-running MCP server kept
resolving imports by the old mapping, and so did later processes: a sync
re-resolves only the changed files, and a config-only edit changes none.

The index now carries a snapshot of the config files resolution read: every
tsconfig / jsconfig the alias loaders opened, `extends` chains included,
every go.mod, and the root's candidates whether present or not. Every sync
reads them again and, when one differs, drops the resolver's alias and
module maps with the memos resolved through them, re-opens every import the
file governs (the ES-module family for a tsconfig / jsconfig, Go for a
go.mod) for the sweep, as a moved workspace map does, and marks synthesis
for a rebuild. An index an older engine stamped records a snapshot without
re-opening anything.

Review changes: each file's digest covers what resolution reads from it, a
go.mod's module path and a tsconfig / jsconfig's `extends`, `baseUrl` and
`paths`, not its bytes. A dependency bump in go.mod or a `strict` flag in
tsconfig had re-opened every import of the language for the same graph
(caddy: 48,945 refs, sync 3.8 s against 0.9 s; excalidraw: 88,860 refs,
9.2 s against 1.1 s). Plus a test for that, the ReferenceResolver class doc
comment back on its class, and the CHANGELOG entry beside the workspace-map
one.

Validation: 7 tests; on main's source the 5 behaviour tests fail, and the
new one fails on the byte digest. 11 fixture edits, each compared with a
fresh index of the same tree, in a later process and in the same process:
main diverged in 7 and 9, this in none. Real repos, sync against a fresh
index over nodes, edges, refs and files: excalidraw with `@excalidraw/math`
retargeted was 27 edges off on main and is identical here; caddy with its
module path renamed was 6,511 edges off and is identical here. Fresh indexes
are identical to main's. A one-file sync on excalidraw, median of 5
interleaved runs: main 3,834 ms, this 3,269 ms.

Original PR #2984 by @danusha2345.
Fixes #2977

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 10:57:07 +00:00
Colby MchenryandClaude Opus 5.5 29ce0149cf fix(lock): only one process takes over a stale write lock (#3056)
Issue #2979: FileLock.acquire() read the lock file, saw a dead PID,
unlinked the file and created its own with an exclusive create. Two
processes that read the same dead PID could both succeed: the first one
replaced the stale lock, then the second one, acting on what it had read
a moment earlier, unlinked the first one's live lock and created its own.
Both returned from acquire() and wrote to the index as its only writer.
The same steal happened in two narrower ways: a lock file read in the
instant between its exclusive create and the write of its PID was empty,
so it counted as stale, and a PID the process may not signal (EPERM:
another user's process, or an elevated one on Windows) counted as dead.

The fix keeps the lock file and its format (a bare PID) and changes how
it is taken:
- A free lock costs one create, as before. The lock file is created with
  its PID already in it: a private file hard-linked into place, which
  fails if the lock exists. Where hard links are missing it falls back
  to the exclusive create, and an empty lock younger than 10 s counts as
  held, since its creator is still writing its PID.
- A stale lock (dead PID, malformed, or empty and old) is replaced only
  by the process holding <lock>.break, itself a FileLock, after reading
  the lock again there, the way Mercurial breaks its locks. A break lock
  a crashed process left is broken the same way, one level up, at most
  three levels.
- EPERM from a signal-0 probe means the holder is alive.

Validation: __tests__/filelock-stale-takeover.test.ts runs two real
processes with a barrier: the slow one stops right after reading the
dead PID and resumes only once the other holds the lock. On main both
held it, 5 runs of 5; with the fix the slow one is refused and the lock
stays the holder's. The other cases cover the slow one getting in once
the lock is free, a live and a dead break lock, the empty-lock window,
EPERM (mocked, and for real on Windows with the System process), and no
leftover files.

Fixes #2979

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 10:40:44 +00:00
Colby MchenryandClaude Opus 5.5 bc9291afe6 fix(java): a call on a value a type holds in a static field reaches the method of the field's type (#3055)
A Java call written through a type's static field, Consts.HELPER.go()
or Holder.SHARED.run(), was resolved by the method's name alone: the
receiver Type.FIELD said nothing of its type, so the call went to a
same-named method of whatever class the name matcher found, and a field
of a library class (Intent.ACTION_VIEW.equals(...), System.out.print())
could reach a project method of that name. An interface's constants were
not indexed at all (neither engine read a constant_declaration), so a
constant a type declares in an interface, or inherits from one, had no
declaration to read.

A Java Type.FIELD.m() (Outer.Inner.FIELD.m(), a package written in
front) now finds the type as the calling file names it (javaTypeRef),
then the field, the type's own or one it inherits (five levels up), and
calls the method on the value the field's declaration gives it, read
with the field's own file's imports: an enum constant's own override,
else the enum's method; the method of the anonymous class the field is
initialized with (a CREATOR's createFromParcel); the class a new X(...)
initializer builds; else the type the declaration writes. A Kotlin
object's INSTANCE or Companion reaches the object's member. A library
owner, or a field of a library type, links nothing. A receiver whose
head is a local or a field links as before. Both engines index an
interface's constant_declaration as a static final constant.

Validation:
- java-static-field-receivers.test.ts: 9 tests, 7 fail on main 60b0d7a9
  (two already pass there: a field typed by its own declaration and an
  anonymous class's method), all pass here.
- Kernel parity (java), 0 files with diffs: Torture.java 1/1,
  TortureRecord.java 1/1, jextract 218/218, spring-modulith 682/682,
  SystemUI 1141/1141, okhttp 71/71, Minestom 1859/1894 (deferrals are
  main's).
- A/B against main 60b0d7a9, sites added/removed/retargeted (conf-only):
  Minestom +26003/-8/122 (751; 12,584 interface constants now indexed,
  409 calls typed), spring-ai +14/-21/786 (823; 719 enum constants' own
  overrides), kestra +27/-273/14 (37), playframework +5/-1/0 (21),
  SystemUI 0/-11/0 (2), spring-modulith +5/-3/4 (26), jextract
  +1/-9/6 (1); okhttp, nowinandroid, mihon, click, gin, serilog
  identical. The removed sites are guesses on library fields and
  methods (kestra's HttpStatus.X.getCode() x180).
- Cost (median of 3 interleaved): SystemUI CPU 92.0 -> 93.7 s, wall
  59.4 -> 58.6 s; Minestom CPU 46.7 -> 56.4 s, wall 17.5 -> 19.4 s, as
  its graph grows by the generated registries' 12,584 interface
  constants (29% more nodes, 30% more edges).

Reimplements #1949 by @mixxer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 09:46:25 +00:00
Colby MchenryandClaude Opus 5.5 7021de5c30 fix(rust): calls through a type a path or a use names reach that type's own function (#3025)
A Rust call through a type, `sim::items::ItemPool::for_def(…)` into another
crate of the workspace or `ItemPool::for_def(…)` under `use
sim::items::ItemPool;`, was matched by its qualified name alone, so a
namesake type's function in another crate or module could take it (a
workspace's `client` crate's `ItemPool::for_def`). The module walk stopped
at the type, a `use` of a `pub const` or `static` (`use sim::RANK_COUNT;`)
linked nothing, and a type rustfmt wrapped below its path (`h:
&scheduler::\n Handle`) linked by the file's `use` of its last name.

The fix, on the module walk:
- rustPathTarget reads `Type::member` calls: the type is the item the
  path's modules name, or the one the `use` that binds its name names
  (rustUseItemsAt), and rustTypeMember finds its member: an enum's variant;
  else the type's own (inherent) function or `const` in the type's crate,
  a trait impl's only when it is the one of that name; a trait's own
  declared method. A type alias, `Self`, a type the module declares itself
  and a type path in any other position are left as they were.
- Module items include `variable`s (a module-level `pub const`/`static`).
- matchRustUseBoundName reads a qualifier written on the line above a
  type (rust-scopes' blanked code, so a commented-out path is none) and
  resolves the whole path.
- Memoized per (type, member) and per path.
- Manifest paths stay inside the project: a workspace member that leaves
  it (`../sibling`, an absolute path) is neither read nor listed
  (escapesRoot, in expandMembers), and rustCrateGraph drops a
  `[lib]`/`[[bin]]` path that leaves it, as it already did a dependency's.

Validation:
- rust-cross-crate.test.ts (PR 2631's 9 cases, credited),
  rust-type-member-paths.test.ts and rust-manifest-paths.test.ts: on main
  10 of 15 fail; all pass. Every rust-* suite passes. On main the workspace
  map read `../outside/Cargo.toml`, `../vendor/x/Cargo.toml` and
  `/abs/crate/Cargo.toml` and listed `../vendor`; now only the project's.
- A/B against main, native kernel, 7 Rust repos (every site the same
  as against PR #3014's own commit; re-checked on 60b0d7a9): tokio +205
  links / 139 retargeted / 230 chains gaining their head call, ripgrep
  +155 / 13 / 1, axum +25, clap +179 / 0 / 295, serde +28, dioxus +142 /
  6 / 31, gleam +114 / 47 / 0; 0 removed. Retargets go to the type the
  code imports or its own crate's (tokio's Semaphore::new and loom mocks
  to tokio::sync, ripgrep's Error::from, gleam's Printer::new); express
  and flask byte-identical.
- Cost, native kernel, medians of 3 interleaved runs (dioxus of 7):
  tokio CPU 32.1 -> 29.7 s, peak RSS 1,000 -> 1,010 MB; gleam 29.1 ->
  28.1 s, 1,010 -> 1,004 MB; dioxus 38.7 -> 40.1 s, 1,111 -> 1,115 MB
  (timed on one thread, rustPathTarget 1.24 -> 1.32 s over 17,198 calls).

Builds on PR #2631 by @BGamboa13.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 09:28:10 +00:00
Colby MchenryandClaude Opus 5.5 cdfa31be54 fix(ruby): a call on an instance variable that initialize types links to its class's method (#3053)
Both extractors record a Ruby call on an instance variable as
`@writer.flush`, and no strategy read the variable's type, so every such
call stayed unresolved: 2,780 in activesupport and 3,239 in actionpack on
main, for example.

ruby-constant-paths now resolves `@name.m` written in an instance method of
a class (not a class method, not a module) by the class's `initialize`.
When every assignment to `@name` there starts a statement and is a lone
`Const.new(...)`, `A::B.new` or `::Foo.new ...` of one constant
(arguments with or without parentheses, a block or a statement modifier
may follow), the class is the one Ruby's constant lookup finds for it from
`initialize`, and the method is that class's own instance method or the
first its ancestry declares. Anything else leaves the variable untyped for
the other strategies, as before: a conditional, two classes, `.tap`,
`writer || Foo.new`, `@a, @b = ...`, a chain continued on the next line. A
class the project doesn't declare (`Logger.new($stdout)`) links nothing.

Validation, kernel engine, main 3a4cd3bf vs this change:
- jekyll 97c3bdc +8, activesupport +19, actionpack +14, activerecord +30
  (rails 793d744 subtrees), sinatra cb22afd 0; nothing removed. 68 of the
  71 are right; 3 in activerecord follow `@pool = NullPool.new` from
  `initialize`, which `pool=` later replaces with the real pool.
- Controls requests (Python) and cobra (Go): dump-graph byte-identical.
- New tests fail with main's resolver (the positive case, in both engines)
  and pass with the fix; the untyped and outside-class cases pass on both.
- Index time, median of 3 interleaved: activesupport 4.72 vs 4.79 s,
  activerecord 11.54 vs 11.54 s.

The gap was found in the triage of PR #684.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 08:37:36 +00:00
Colby MchenryandClaude Opus 5.5 6d3804cf57 fix(resolution): C, C++ and Objective-C rank as one language, and a lone candidate is judged by family (#3052)
Name matching compared a candidate's raw language tag with the
reference's: the single-candidate confidence in matchByExactName and
matchFuzzy, and findBestMatch's same-language skip and +50/-80 score.
So a call whose name had several definitions in another of C, C++ and
Objective-C scored -80 for each and linked to nothing (an Objective-C
file's _glfwPlatformSetTls(), a C++ call into Dear ImGui's imgui.h, which
reads as C), and the one definition of a name across TSX and TS, or C and
C++, was a 0.5 cross-language guess.

The single-candidate confidence now compares language families
(sameLanguageFamily). Ranking treats C, C++ and Objective-C as one
language (sameRankingLanguage), the very language worth a point that only
breaks a tie; other families keep the language itself, because ranking
them by family moved excalidraw's Store::scheduleCapture calls to the
App.tsx method beside them and gave okhttp 83 wrong Java-to-Kotlin
Builder picks.

Validation:
- __tests__/name-match-language-family.test.ts, 8 tests (default and
  wasm): 6 fail on the base main; the pin that a .ts call keeps its .ts
  target over a .tsx namesake beside it passes on both; all pass with
  the fix. 24 related test files (cross-language, React Native, Expo,
  Fabric, frameworks, mixed TS/JSX, Objective-C, resolution): 746 pass.
- A/B, main vs fix: glfw +4 calls from Objective-C into C, imgui +93
  from C++ into imgui.h (read as C) and imstb_rectpack.h, all to the
  definitions meant; excalidraw, okhttp, leveldb and jq gain or lose no
  edge (43, 9, 97 and 30 unique-name links go from 0.5 to 0.9 with the
  same targets); flask and gin byte-identical.
- Index time, median of 3 interleaved: imgui 7.9 s main, 7.7 s fix;
  excalidraw 9.2 s main, 9.4 s fix.

Reimplements PR #1662 by ferrine.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 08:15:23 +00:00
Colby MchenryandClaude Opus 5.5 19b74d10f3 fix(deps): read .gitignore rules the way git does, with ignore 7.0.14 (#3050)
codegraph applies .gitignore rules itself, through the ignore package:
on the filesystem walk for every .gitignore, and in git repositories on
top of git ls-files for its built-in defaults merged with the root
.gitignore and git's exclude files. codegraph.json's include, exclude
and includeIgnored patterns go through it too. ignore 7.0.5 read several
forms differently from git: a backslash escape (\d was a regex digit),
POSIX classes and a ] or ! first in a bracket, and a run of three
asterisks. A lone ! line matched every path, so it re-included
everything the rules and the built-in defaults leave out, node_modules
included. 2,031 of 200,000 random patterns also threw at match time,
which readGitignorePatterns has to guard against (issue 682).

ignore 7.0.14, with the range raised to ^7.0.14, reads all of these as
git does, and none of the 200,000 patterns throws. Its code diff from
7.0.5 was read in full: pattern translation only, with no I/O, no
dependencies and no install scripts. The lockfile entry matches the npm
registry's own metadata on registry.npmjs.org. The package has no
provenance, like every release its maintainer has published.

Validation:
- New __tests__/gitignore-pattern-parity.test.ts checks scanDirectory
  against git's own answer for these patterns, on the filesystem walk
  and in a git repository: its 4 tests fail with 7.0.5 and pass with
  7.0.14.
- scanDirectory on react, astro and django, in git mode and in walk
  mode on a copy without .git, returns the same 4,631, 4,946 and 3,027
  files with either version.
- On a fixture of the changed forms, 7.0.14 leaves out exactly what git
  leaves out in both modes, node_modules aside, which codegraph's
  defaults always exclude. With a lone ! line, 7.0.5 kept 16 of the 18
  files on the walk, node_modules among them, where git keeps 6. Without
  that line it differed from git on 8 files on the walk and on 2 in git
  mode.
- The gitignore and scope test files (extraction,
  git-ignored-dirs-scope, the include, exclude and includeIgnored
  configs, src-build-folders and others): 853 passed.

Raised by PR 2885 (@johnhldiver-beep).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 07:49:46 +00:00
Colby MchenryandClaude Opus 5.5 2514467801 fix(jvm): a dotted supertype names its nested type, and a Kotlin object expression is an anonymous class (#3051)
A supertype written through its enclosing type was lost in three ways.
Java and C# kept the dotted path (class Named extends Outer.Inner,
class N : Outer.IListener), but the qualified-name match compared it
verbatim with p::Outer::Inner, so it stayed unresolved; a Java anonymous
class (new Api.Listener() {...}) kept only the last segment, which no
nested type is found by; and Kotlin (both engines) took the FIRST
segment, so class K : Outer.Inner() extended Outer. A Kotlin object
expression, object : Listener {...}, made no class at all: its overrides
became local functions of the code around it, which a call through the
interface never reached, and bare calls elsewhere could be guessed onto
them.

A dotted Java, Kotlin or C# supertype now resolves to the type whose
qualified name ends with the path, when the file can name the path's
first type (its own file, package or namespace, an import; C#'s usings);
of several, the one closest in the tree, or none on a tie. The Java
anonymous class keeps the written path in its extends reference, and
Kotlin joins every segment of a supertype (type arguments left out), in
the wasm extractor and the kernel alike. A Kotlin object expression is
indexed as Java's anonymous class is: a class <Listener$anon@line> that
extends each supertype as written, which the code around it
instantiates (the class it builds, else its first supertype, also as
written and only ever a type that can be a supertype), with its body's
declarations as members; its header (constructor arguments, a
by-delegate) stays the enclosing code's. An anonymous class's members,
Java's and Kotlin's, are named only inside the declaration holding the
class: a bare block() elsewhere is never an object's override val block.

The walk up a Java or Kotlin class's supertypes for an inherited method
asks each supertype by the chain of types that names it
(AssistantMessage::Builder) before its simple name, so a builder's
build() is its own AbstractBuilder's and not an MCP annotation's;
the name still answers when an extends edge reached a namesake
(Minestom's Player extends LivingEntity).

The code in an object expression still sees the scope it is written in,
as when its overrides were local functions: a property of the class
around the object types a receiver there (okhttp's server.url() in an
object : Callback is MockWebServer's), an override is not what a call
of its own name in it means (original!!.contentLength(),
this@Outer.onScroll(), an extension receiver's onDataChanged()), and an
object's members out of reach leave a by-name guess as it was
(okhttp's it.isReady() is still the SerialTask interface's).

Validation:
- jvm-dotted-supertypes.test.ts: 13 tests, 11 fail on main 60b0d7a9
  (the other two guard a dotted supertype the file cannot name and the
  calls inside an anonymous class), all pass here.
- Kernel parity, 0 files with diffs: torture.kt 1/1, Torture.java 1/1,
  okhttp 588/619 Kotlin and 71/71 Java, mihon 891/940, nowinandroid
  340/350, SystemUI 188/198 Kotlin and 1141/1141 Java, jextract 218/218,
  Minestom 1859/1894 (deferrals are main's).
- A/B against main 60b0d7a9, sites added/removed/retargeted: okhttp
  +640/-53/149, SystemUI +435/-53/116, Minestom +165/-3/6, kestra
  +108/-0/6, spring-ai +46/-0/38, playframework +27/-3/13, mihon
  +22/-5/6, jextract +22/-0/1, spring-modulith +9/-0/10, nowinandroid
  0/0/0; serilog, click, gin identical.
- Cost (median of 3 interleaved): okhttp CPU 27.8 -> 29.0 s, wall
  8.6 -> 8.8 s (its 360 object classes and 1,491 more edges); mihon
  23.6 -> 23.8 s, wall 7.8 -> 7.7 s.

Reimplements #1927 by @mixxer.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 07:29:52 +00:00
Colby MchenryandClaude Opus 5.5 1941caf7bc fix(add-lang): the extraction check finds codegraph's npm shim on Windows, and takes CODEGRAPH_BIN (#3047)
scripts/add-lang/verify-extraction.mjs ran execFileSync('codegraph', ...).
On Windows, npm installs codegraph as a .cmd shim (so do npm link and
local-install.sh), and Node neither finds a .cmd by bare name nor runs
one without a shell. The check always died with "spawnSync codegraph
ENOENT" (exit 2), and /add-lang's bench.sh read that as broken
extraction and skipped its A/B.

The script now asks, in order:
- CODEGRAPH_BIN, when set. A .js, .mjs or .cjs path runs with the
  current node; anything else runs directly (a .cmd or .bat through
  cmd.exe).
- On Windows, the codegraph Windows itself would pick: the first PATH
  folder holding codegraph under one of PATHEXT's runnable extensions.
  A .cmd or .bat runs through cmd.exe (shell: true) as one command
  string. Each token is quoted for the C runtime and caret-escaped for
  cmd, so spaces, &, parentheses, a %NAME% and a trailing backslash in
  the repo path arrive intact. An .exe or .com needs no shell.
- Otherwise codegraph by bare name, exactly as before. On macOS and
  Linux without CODEGRAPH_BIN, the call and the output are unchanged.

bench.sh takes CODEGRAPH_BIN too. It makes a path absolute (indexing
runs from inside the repo), exports it so verify-extraction.mjs reads
the index with the same build, and runs its own --version and init calls
with it. Without it, bench.sh behaves exactly as before. The A/B's MCP
server stays run-all.sh's own CG_BIN.

Validation (Windows 11, Node 22.22.0):
- New __tests__/add-lang-verify-extraction.test.ts covers CODEGRAPH_BIN
  with a .js stand-in (all platforms), a .cmd shim on PATH with an
  awkward repo path (Windows only), and the bare-name call (macOS and
  Linux only). With main's script both tests that run here fail ("could
  not read codegraph status"); with the fix, 2 pass and 1 is skipped.
- The fixture from PR 1246's review (a codegraph.cmd on PATH): main
  exits 2 with ENOENT; the fix reads the status.
- 13 scenarios with npm's own generated shims, and a real index in a
  folder named "lua repo & co (x86) 100%": main fails every one that
  needs the shim or CODEGRAPH_BIN, and the fix passes them with the
  exact argv reaching codegraph. With no codegraph anywhere, both exit 2
  the same way.
- bench.sh with the A/B stubbed: with npm link's shims on PATH, main's
  copy skips the A/B (verify exit 2) and the fix reaches it (PASS).
  CODEGRAPH_BIN as an absolute or a relative path reaches it too, and a
  missing one stops with a clear message.
- With process.platform reported as linux or darwin, main's script and
  the new one make the same execFileSync call and print the same output.

Raised by PR 1246 (@bslatner).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 07:27:10 +00:00
Colby MchenryandClaude Opus 5.5 4e7a221089 chore(deps): take the security fixes for devalue and postcss, drop an unused types package (#3044)
devalue 5.9.1 (root, through svelte) and 5.8.1 (site/, through astro)
fall in seven advisories published 2026-10-01 and fixed in 5.9.3, among
them GHSA-j22f-vq7h-c4qm (CVE-2026-92708, high). postcss 8.5.6 (root,
through vite) and 8.5.15 (site/) fall in GHSA-r28c-9q8g-f849
(CVE-2026-73646, high, fixed in 8.5.18) and GHSA-fxqj-rqcc-2cmp (fixed
in 8.5.23); the root copy also in GHSA-6g55-p6wh-862q and
GHSA-qx2v-qp2m-jg93. All of these are build-time dependencies.

Lockfile-only updates inside the existing ranges: npm update devalue and
npm update postcss, in the root and in site/. devalue goes to 5.9.4 and
postcss to 8.5.32, whose own ranges move nanoid to 3.3.20 and
source-map-js to 1.2.2, which clears their advisories as well
(GHSA-28wg-ghj8-5hjv, GHSA-2v37-7h3g-55p8, GHSA-68fv-2mgg-jv7q). The
@types/better-sqlite3 devDependency goes: nothing has imported
better-sqlite3 since the switch to node:sqlite. In site/, npm 10 also
drops five "peer": true markers that the npm which wrote that lockfile
had added; they are metadata only, and npm ci installs the same tree.

Validation:
- npm audit: root 14 advisories before, 10 after; site/ 13 before, 9
  after. devalue, postcss, nanoid and source-map-js are gone from both.
- npm run build on main's lockfile and on this one: all 1,264 files of
  dist/, the viewer included, are byte-identical. The site builds its
  21 pages, and its 101-file dist/ is byte-identical too.
- The release bundle's install (npm ci --omit=dev --ignore-scripts on
  the staged lockfile) installs the same 12 packages, file for file.
- All 8 changed resolved/integrity entries match the npm registry's own
  metadata and sit on registry.npmjs.org. No git, URL or tarball
  sources, and no new install scripts. devalue, postcss and nanoid carry
  provenance from their own repositories' release workflows.

Raised by PR 2885 (@johnhldiver-beep) and PR 1477 (@anupamme).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>


[skip actions]
2026-10-30 07:13:13 +00:00
Colby MchenryandClaude Opus 5.5 3a4cd3bf65 fix(ruby): calls to !/? methods and calls on what .new made link their method (#3049)
Two kinds of Ruby call linked nothing. A call to a method whose name ends
in `!` or `?` on a receiver (`writer.flush!`, `writer.ready?` after
`writer = CacheWriter.new`, `CacheWriter.create!(1)`) failed the method-call
pattern, whose method part took no `!` or `?`. A method called straight on
a new object (`CacheWriter.new(key).write_cache`, `Billing::Ledger.new.charge!`)
was recorded by both extractors with the receiver's raw text, arguments and
blocks included, which no strategy matched.

Both extractors now record a call on `Const.new(...)`, `A::B.new` or
`::Foo.new` as `new Const().m`, the constructed-receiver shape TS/JS, Java
and C# already use; the wasm extractor and the kernel's ruby.rs emit the
same refs. ruby-constant-paths resolves that shape before the name
pre-filter: the class by Ruby's constant lookup from the namespaces around
the call, the method as the class's own instance method or the first its
ancestry declares, and nothing when either is missing, so rack-protection's
`Request.new(env)` (rack's Rack::Request) links nothing. The Ruby dot pattern
in matchMethodCall takes a trailing `!` or `?`; the receiver-word scoring
among several project methods of the name stays off for such names on a
value receiver, where it was wrong on 55 of 74 new edges (`options.key?`
on a Hash -> InheritableOptions#key?). rubyAncestry no longer reads a
module a call returns (`include RouteSet.new.tap {...}.url_helpers`) as a
mixin of the constant the call starts at.

Validation, kernel engine, main 37052b18 vs this change:
- sinatra cb22afd +12, jekyll 97c3bdc +53, activesupport +398,
  actionpack +97 (2 removed: `ActionController::Base.with` had reached
  RoutesHelpers.with through a misread mixin), activerecord +1012
  (rails 793d744 subtrees). About 21 of 1,572 added edges are wrong, all
  from the class-name and single-method guesses that plain names get too.
- Controls requests (Python) and cobra (Go): dump-graph byte-identical.
- kernel-parity.mjs: fixtures 10/10, sinatra 147/147, jekyll + rails
  1044/1044 files byte-parity, none deferred.
- New tests: 10 fail with main's kernel and TS, all pass with the fix, in
  both engines. Dropping the scoring gate or the mixin fix fails its guard
  test.
- Index time, median of 3 interleaved: activesupport 5.35 vs 4.63 s,
  jekyll 2.66 vs 2.73 s (noise).

Reimplements PR #684 by @ricobl, who found both gaps.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 06:47:47 +00:00
Colby MchenryandClaude Opus 5.5 b700a3eec2 fix(python): a parameter or local named like an imported module is not that module (#3046)
A Python call through a name the file imports as a module, like
other.update(...) after `from pkg import other`, linked to the module's
function whatever the calling function bound `other` to: a parameter, a
local, a with/except/loop target, a walrus, a case capture, a lambda or
comprehension variable. resolveViaImport read the file's import mappings
alone (its only scope check, pythonFunctionModuleAlias from PR #2600,
covers a function-local `import a.b as X`), and isPythonProjectModule,
which lets a builtin-named call like update/get/write past the builtin
filter for a project module, asked the same file-wide question. The
mappings also list from-imports at any depth ahead of plain imports, so a
function-local `from pkg import third as other` became every function's
`other`.

pythonReceiverBinding reads how the code around a reference binds the
name: the reference's own statement (lambda parameters, comprehension
targets), then each enclosing function, innermost first, through its
parameters and own statements (assignment, annotation, for, as, walrus,
del, nested def/class, case captures, imports; global keeps the module's
binding), memoized per function. pythonImportsInScope gives
resolveViaImport's Python branch and isPythonProjectModule only the
receiver's mappings that apply there.

Validation:
- __tests__/python-receiver-rebinding.test.ts, 80 tests (default and
  wasm, LF and CRLF): 48 fail on the base main (ten rebinding shapes,
  the local from-import, the cross-function leak), 32 pass (look-alikes:
  keyword argument, string, comment, comprehension over the module, lambda
  beside the call, global, keyword pattern, same-module local import);
  all pass with the fix. The 26 Python-related test files pass.
- A/B, main vs fix: django's own package (930 files, kernel path) changes
  2 edges' confidence (0.85 to 0.8, same targets: a closure over a
  parameter `apps` and a local `apps = model._meta.apps`); flask drops
  one cli.group() call and lowers 4 to 0.7 with the same targets (a
  nested `def cli` and a pytest fixture parameter `app` named like
  imports); requests, click, mealie and fastapi (package plus tests), and
  the express and gin controls are byte-identical.
- django package index time, median of 3 interleaved: 11.3 s main,
  10.7 s fix.

Reimplements PR #2632 by BGamboa13.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 06:22:47 +00:00
Colby MchenryandClaude Opus 5.5 407ec4fba2 chore: keep the kernel's vendored grammars out of GitHub's language stats (#3045)
GitHub reports the repository as 79% C and 18% TypeScript. Nearly all of
that C is the third-party tree-sitter grammars the native kernel compiles
from source (codegraph-kernel/grammars/, 29 files, about 78 MB).

A new .gitattributes marks every file under codegraph-kernel/grammars/
linguist-vendored, so Linguist leaves them out of the language
statistics, and marks the five generated parser.c files
linguist-generated, so pull requests show those collapsed. The
hand-written scanner.c files stay expanded in diffs on purpose: that is
where C gets patched or added (PR 2173, and the open PR 2866), and every
contributor PR is security-reviewed, so such a change must stay visible.
The patterns use /** because an attributes pattern that names a
directory does not reach the files inside it.

Validation: git check-attr over all 1,722 tracked files reports
linguist-vendored set on exactly the 29 files under
codegraph-kernel/grammars/ and linguist-generated set on exactly the
five parser.c files; scanner.c, the headers and the LICENSE files are
vendored only, and everything else, src/index.ts included, has neither.
In a scratch repository the bare directory pattern leaves parser.c
unspecified. Git does not act on linguist attributes and codegraph never
reads .gitattributes, so builds and tests are unaffected.

Raised by PR 2513 (@build8421) and PR 1668 (@kidonng).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 06:14:08 +00:00
Colby MchenryandClaude Opus 5.5 37052b1825 fix(go): a package-level var or const named in uppercase is exported (#3043)
Both extractors created a Go var/const node from its var_spec or
const_spec without exportedness: the TS Go branch passed no isExported
(the declaration-level value is read off the var_declaration, which has
no name), and the kernel's extract_variable set none. Every such node was
unexported, so findGoPackageMember, which looks up pkg.Name among the
package's exported declarations, skipped it: a call through
`var Hook = func...` from another package linked to nothing, though the
same call inside the package linked to the variable.

Both engines now mark the node exported by its own name's case, read
from the spec through goExtractor.isExported / is_exported, as
functions, methods and types already were.

Validation:
- __tests__/go-package-value-exported.test.ts, 16 tests (extraction on
  the kernel and wasm, LF and CRLF; cross-package calls on both paths):
  12 fail on the base main, 6 with only the TS half (the kernel
  checks), all pass with the fix.
- A/B, main vs fix, kernel path: gin 108 var/const flags, 0 edges;
  prometheus 625 flags, 0 edges; etcd 806 flags and 12 new calls,
  all right (e2e.GetVersionFromBinary x11 and
  model.NonDeterministicModel, both `var X = func(...)`); flask and
  express byte-identical. The fix's kernel and wasm graphs are
  byte-identical on all three Go repos, and the wasm A/B matches.
- kernel-parity --lang go: gin 99/99, prometheus 755/755, etcd
  1065/1105 with 40 deferred on main too; 0 diffs.
- etcd index time, median of 3 interleaved: 13.4 s main, 12.6 s fix.

Reimplements PR #1521 by ericquan8.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-30 06:01:18 +00:00