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>
Replaces the old interactive publish.js script with two Claude skills and
a full agent-evaluation harness:
- `.claude/skills/audit/` — `/audit` skill drives `scripts/agent-eval/audit.sh`
to benchmark retrieval quality (with vs. without codegraph) on a chosen
real-world repo from the new `corpus.json` (17 repos across 14 languages).
- `.claude/skills/publish/` — `/publish` skill orchestrates the full release
workflow (preflight → changelog → confirmation gate → bump/build → npm
publish → GitHub release), replacing `publish.js`.
- `scripts/agent-eval/` — headless (`run-agent.sh`, `run-all.sh`) and
interactive tmux (`itrun.sh`) harnesses with stream-json parsers
(`parse-run.mjs`, `parse-session.mjs`) that report tool calls, token
usage, and a VERDICT line summarising codegraph_explore vs. Read/Grep counts.
- `run-interactive-test.md` — documents the two harnesses, idle-detection
approach, and what "good" agent behavior looks like after explore-first
guidance.
