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>
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>
