Cognee Code Graph

Use this skill when the user asks Codex to build a Cognee memory of a repository, index code, or answer structural code questions (who calls X, what breaks if X changes, how does A reach B) from memory.

Requires a Cognee server >= 1.5.3. Indexing runs the enola code-graph pipeline server-side and makes no LLM or embedding calls — it is fast, deterministic, and token-free.

Rules

• Server-first: the scripts below POST to the running Cognee server. There is deliberately no CLI fallback for code indexing/search — an unreachable server means "not done", never "index some other way".
• One narrow dataset per repository (default codebase-<repo-name>-<digest>); do not mix repositories into one dataset. The digest is the indexed path, so two checkouts sharing a basename stay in separate graphs. --code searches resolve the name from the current checkout, so it rarely needs to be typed.
• Never index directories holding secrets you would not ingest as documents; the pipeline skips .env/dotfiles/binaries itself, but a git URL to a private repo still lands its code in the target dataset.

Index a repository

${CODEX_PLUGIN_ROOT}/scripts/cognee-index-repo.sh <repo-path-or-git-url> [--dataset <name>] [--index-vectors] [--wait <seconds>]

• Local path (e.g. .): works when the Cognee server shares this filesystem — the default local plugin server does. Cloud servers reject local paths; pass a git URL instead.
• Git URL: the server shallow-clones it; freshness follows pushed commits (local edits are invisible to it).
• --index-vectors: also embeds the code facts so semantic/hybrid search can see them (needs an embedding provider). Without it, code knowledge is reachable ONLY through code search below.
• The submit returns quickly (background pipeline); --wait 60 polls pipeline=code_graph_pipeline until queryable.

Indexing writes enola's snapshot to <repo>/.enola/ (untracked) — add it to .gitignore or global excludes. The plugin's change detection ignores it.

Indexing is also the freshness opt-in: for local-path repos the plugin records a git fingerprint and automatically re-submits the repo in the background when a turn changed the working tree. Re-running the command on an unchanged repo is skipped server-side (content hashes), so it is always safe.

Automatic indexing

Opening the agent inside a git repository indexes it automatically in the background at session start — no setup step. What happens depends on the server, because indexing a repo means the code has to be readable by it:

Situation	Behavior
Local server (default), new repo	Indexed automatically — the server reads the working tree in place, so the code never leaves the machine
Cloud/remote server, new repo	Not indexed automatically; run the index command with a git URL, or set COGNEE_CODE_AUTOINDEX=always
Already-indexed repo	Always refreshed if the tree changed since the last index — regardless of the setting above
Not a git repo / no code files / very large repo (>3000 source files)	Skipped; index it explicitly if you want it

Set COGNEE_CODE_AUTOINDEX=off to disable automatic indexing of new repos (explicitly indexed repos keep refreshing). Explicit indexing has no size cap.

What the graph reflects (freshness)

The graph tracks different things depending on where the Cognee server runs. Both are normal, expected behavior — but the results look identical, so know which one applies:

Server	Graph reflects	Stays current via
Local (default)	The working tree, uncommitted and untracked changes included	Automatic re-index after any turn that changed a file
Cloud / remote	The last pushed commit — the server clones the repo and cannot read this machine's disk	Pushing, then re-indexing

On a cloud server, local edits are invisible to the graph until they are pushed. Nothing errors and nothing looks unusual: a question about a symbol you just renamed locally is answered from the pushed state, confidently. So when the answer matters and the work is in progress, either push first or say so in the answer. {"operation": "delta"} shows what the last index actually changed and is the fastest way to check what the graph currently knows.

Local-path indexing therefore requires a server that shares this filesystem; cloud servers reject local paths and need a git URL.

Query the code graph

${CODEX_PLUGIN_ROOT}/scripts/cognee-search.sh "<seed>" 10 --code [--code-query '<json>']

Without --code-query, the query text is a seed name (exact/suffix/substring match). With it, pick one exact operation:

Operation	Answers	Example
query_facts	filtered listing	{"operation":"query_facts","kind":"route","limit":50} — all API endpoints
explore	neighborhood of one node	{"operation":"explore","name":"UserService","max_depth":1}
traverse	follow edges from seeds	{"operation":"traverse","start":"main","direction":"forward","max_depth":3}
find_path	how A reaches B	{"operation":"find_path","source":"AuthMiddleware","target":"Database"}
impact_analysis	what breaks if X changes	{"operation":"impact_analysis","targets":["process_payment"]}
delta	what the last index changed	{"operation":"delta"}

An ambiguous seed returns an error listing the candidates — retry with an exact id or a repo filter. A seed that doesn't resolve returns empty (not an error): the graph has no such symbol.

When to use which search

• Structural question naming a symbol/file → --code. Exact, instant, no tokens.
• Conceptual question naming nothing ("how does auth work here?") → regular cognee-search.sh (hybrid/graph). Graph-only code is invisible there unless indexed with --index-vectors or the repo's docs were ingested as documents.
• Chain them: hybrid discovers the name, --code gives the exact structure around it.
• Verify freshness: after edits, {"operation":"delta"} shows what the last re-index added/updated/removed.

Treat results as a map, not ground truth — verify important claims against the actual files before editing code.

Per-file ingestion (no repo index)

To store a single code file in normal memory under its real filename (routes down the zero-LLM code path server-side, no cross-file edges):

${CODEX_PLUGIN_ROOT}/scripts/cognee-remember.sh --file src/payments.py --node-set project_docs

Prefer the repo index above when callers/imports across files matter.

Automatic recall

Once a repo is indexed from its checkout, the per-prompt memory recall adds a code lane automatically when the prompt mentions an identifier-shaped token — the facts appear in the injected context as === Code graph facts ===.