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Use this page when entire-graph is not installed, not being used by your agent, or not returning what you expect.

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Install and Setup

The plugin is not installed. The CLI does not recognize graph as a command, so it falls back to its own help output.
Confirm it landed:
Your Git is older than 2.36. entire-graph uses the single-session object protocol that Git 2.36 added to check an object’s type before reading its contents, so queries cannot run without it. The error names the requirement:
Check your version, and upgrade Git if it is older:
If several Git installations are present, confirm which one entire-graph resolves on your PATH:
You are running an unversioned local build, usually from scripts/install-local.sh or a manual go build. That is expected during development and not expected otherwise.Reinstall a released build:
Releases are verified against the release’s checksums.txt. A release that publishes no checksums is refused.If you trust the source and understand the tradeoff, pass --allow-unverified. Otherwise check that you have the right repository URL.Installing from a URL that is not in the plugin index also asks for confirmation. In a script or CI, add --yes.
init-agents checks both instruction files before its first write, so a failure means nothing was changed.Two things cause it. First, AGENTS.md or CLAUDE.md is not a regular file. A directory, pipe, socket, or device is rejected, and the error names the type it found. Second, a file has a broken marker layout. Each file must contain either zero entire-graph marker tokens, or exactly one begin marker followed by one end marker.Marker tokens count even inside code fences, examples, or HTML comments, because they make the replacement range ambiguous. To recover:
  1. Back up AGENTS.md and CLAUDE.md.
  2. Replace any non-regular target with a regular file, or move it aside.
  3. Reword any stray marker strings that appear in examples or comments.
  4. Rerun entire graph init-agents --repo ..
That file is generated, and it is regenerated in full on every successful init-agents run. Manual edits there are not preserved by design.Put your own instructions in AGENTS.md or CLAUDE.md, outside the <!-- entire-graph:begin --> and <!-- entire-graph:end --> markers. Everything outside those lines is left alone.
Delete .entire/graph-agent.md, then remove the section entire-graph manages in AGENTS.md and CLAUDE.md. You can delete .entire/ or either instruction file if it is otherwise empty.To also remove entire-graph from your machine, run:

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Your Agent Is Not Using entire-graph

This is the most common problem, and it has three usual causes.The session predates activation. An agent session that was already open never read the new files. Quit it and start a fresh session in the repository.The guide is not reaching the agent. Confirm the generated guide matches your installed build:
Empty output means they match. Then check that the managed block is present in the instruction file your agent actually reads.Your agent does not resolve @ imports. Claude Code loads CLAUDE.md at session start and resolves the import. Other clients may treat the block as plain text, in which case they still get a written instruction to read .entire/graph-agent.md, but whether they follow it depends on the client and the model. Verify the behavior rather than assuming it.
If a distinct CLAUDE.md already contains a live standalone import that resolves to your root AGENTS.md, entire-graph deliberately puts only an inheritance notice in its CLAUDE.md block, so the guide is not imported twice:
Add or remove that AGENTS.md import and rerun init-agents to switch between the two layouts. Import detection only recognizes standalone paths. A mention inside inline code, a code fence, or an HTML comment does not count, and anything ambiguous keeps the direct pointer instead of assuming inheritance.

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Queries Are Slow

entire-graph reuses a cached snapshot only when the working tree is clean. Any dirty file that entire-graph can index turns reuse off for the whole repository until the tree is clean again.Clean tree:
One uncommitted change to an indexable file such as go.mod:
Check what is dirty:
Extensionless files and root dependency manifests like go.mod and package.json all count. Dirty files entire-graph cannot index, such as a .bin, do not.The most common version of this is forgetting to commit the three activation files after running init-agents.
Two defaults have to line up, and out of the box they do not.index only warms committed-tree queries, and the interactive commands read the working tree unless you pass --head. index also defaults to --profile full while plain search defaults to --profile fast, and the profile is part of the cache key.So a default index run does not warm a default search. Match both:
Changing .graphignore also selects a different cache entry.
Unlike the other query commands, def and explain only cache when --cache-dir or ENTIRE_PLUGIN_DATA_DIR is set. Set one of them if you are calling those two repeatedly.

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Results Are Not What You Expected

entire-graph lists every definition it found and prints the exact selector for each one, so you can copy the one you want:
You can also address a definition directly with --symbol FILE:LINE.
Usually the name is spelled differently in source, or it lives in a language that is inventory only. Start with search, which takes plain language rather than an exact symbol.
Expected, and worth internalizing. Static analysis is heuristic, not a compiler. Calls through interfaces, reflection, dynamic dispatch, and generated or runtime-wired code can be missed or left unresolved.Dependent counts are guidance for inspection, not facts. Treat graph output as evidence to check against source. Relation edges carry resolution and confidence fields rather than a completeness promise.
entire-graph tells you when the ranking did not actually choose, for example when the top two results are effectively tied:
Rephrase the query to be more specific, or accept that the repository may not contain what you asked for. Do not edit on a low-confidence hit without reading the source first.
Coverage comes in two tiers. Semantic languages are parsed for relationships; inventory-only filetypes give you file and symbol structure but no call or type analysis. See What entire-graph Might Not Find for which languages are in each tier.Check what your build supports:
Files the parser cannot handle surface as machine-readable partial failures rather than vanishing silently. Look at the partial_failures and warnings fields in JSON output, or the coverage line in agent format.Vendored and generated sources that are tracked in Git are the usual cause, since they show up as E_FILE_TOO_LARGE or E_PARSE_ERROR. Exclude them with a .graphignore at the repository root, which uses gitignore syntax and applies on top of .gitignore.

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Checking the Environment

entire graph doctor reports the resolved repository, the Entire environment variables, whether the plugin data directory is writable, and confirms no network egress:
If a script built a command line against a different version, check it before running anything:
An unaccepted flag is named explicitly, without reading the repository or building an index:

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Continue With

Install and Enable entire-graph

Install the plugin and turn it on for a repository.

entire-graph CLI Reference

Every query, analysis, and export command.

plugin

Install, upgrade, and remove plugins.

entire-graph Issues

Report a problem with entire-graph.