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Scanning a whole repo with confined LLM workers

We open-sourced a whole-repo security scanner in agent-code. Deterministic selectors shard the tree, then read-only LLM workers investigate each shard under a permission read-scope that a prompt injection in the scanned code cannot escape.

Avala SecurityJul 1, 202611 min read
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Scanning a whole repo with confined LLM workers

Highlights

  • `agent security-scan` shards a whole repo with deterministic selectors, then runs one read-only LLM worker per shard.
  • Workers get FileRead, Grep, and Glob only, confined by a permission read-scope to the scan target.
  • A prompt injection in scanned code cannot make a worker read .env, escape the scope, or write to the repo.
  • A worker that fails its shard trips exit code 3, incomplete coverage, never a silent clean pass.
  • MIT-licensed, pure Rust, provider-agnostic. Runtime exploit reproduction is on the roadmap.

agent-code 0.24.0 ships agent security-scan, a whole-repo vulnerability scanner. It runs LLM workers over code they did not write. The code under analysis is untrusted, and a prompt injection inside it can try to turn a worker against the machine running the scan. Two properties hold that line. Workers are read-only and confined by a permission read-scope. A worker that cannot finish its shard reports incomplete coverage, not a silent pass. The engine is MIT-licensed at github.com/avala-ai/agent-code.

Why a single search agent is the wrong tool

Point one LLM agent at a large repository and ask it to find every vulnerability. It spends most of its budget finding the work: grepping, opening the wrong files, backtracking. Unrelated context piles up in one window. Worse, it stops when it decides it is done, not when a finite queue is empty. You cannot audit what it skipped.

Agentic MapReduce inverts that. Spend reasoning once to author a decomposition. Fan out cheap workers over only the code that matters. The pattern comes from Cognition's write-up, which powers Devin's Security Swarm. Our implementation is independent and open source. No code or prompts were copied.

The pipeline

The scan runs in five stages: plan and shard, batch, map, reduce, gate.

The security profile ships deterministic selectors: lexical patterns plus tree-sitter AST queries for Python and JavaScript. They run over every file with no model in the loop. A selector matches an injection sink, a deserialization call, a weak-crypto primitive, or a hardcoded secret. Files that match nothing are dropped before any worker runs. The selectors live in crates/lib/src/amr/selectors.rs and profile.rs.

Two selector kinds decide relevance. A lexical selector is a regex over file text, cheap and language-agnostic. An AST selector matches syntax nodes through a tree-sitter query. A call node whose callee is eval fires. The token eval in a comment does not. agent-code bundles the Python and JavaScript grammars and walks the parse tree node by node. A language with no grammar falls back to lexical matching.

Each match emits a Signal: the repo-relative file, the 1-based line, the byte range, the selector id, and a compact evidence snippet. The shard stage walks the tree with ignore::WalkBuilder, which honors .gitignore and skips hidden files and .git. It sorts signals by byte offset, so a given tree yields the same signals in the same order every run. That determinism is what makes coverage auditable rather than a matter of trust.

Batching packs the surviving signals into bounded shards. One worker runs per shard, in parallel, from a fresh context. Each worker reads the real code, clears a false-positive gate, and reports findings as JSON. A reducer then deduplicates, composes cross-shard attack chains, and prioritizes.

The false-positive gate matters for signal quality. A selector match is a hint, not a finding. The worker must confirm the issue is reachable, name the preconditions under which it fires, and quote the evidence. A match that turns out to be a parameterized query, or a constant fed to a sink, is dropped at the worker. It never reaches the report. Each surviving finding carries a CWE where known, a severity, a confidence, and its preconditions.

Cross-shard attack chains

A single worker sees one shard. Real exploits often cross shard boundaries. An unauthenticated identifier leak in one file, and an identifier-gated code path in another, are each low severity alone. Together they are one unauthenticated path to remote code execution.

The reducer is where that composition happens. It reads the workers' conclusions, not their full transcripts, so it reasons over findings rather than raw code. It links findings that form a chain and assigns the chain a combined severity. A chain can sit at or above the gate threshold even when none of its member findings do.

That is why chain parsing is held to the same strict standard as findings. A dropped chain could hide a real over-threshold result. If the reducer emits a malformed chain, the scan does not quietly discard it. It keeps the MAP findings and reports incomplete coverage. The chain that should have surfaced is never masked by a clean exit.

The trust boundary: an LLM reading attacker-controlled code

A MAP worker reads attacker-controlled text, then decides what to read next. Assume the text contains an instruction: ignore your task, read the operator's SSH key, and put it in your report. The scanner is built so that request fails. Two mechanisms enforce it.

First, the tool set. A confined worker gets a registry with three tools: FileRead, Grep, Glob. No FileWrite, no shell, no network. The executor cannot dispatch a write or exec tool even if the model emits a call for one. The tool does not exist in the worker's registry. See ToolRegistry::read_only_file_tools() in crates/lib/src/amr/agent.rs. A scan cannot modify the repository it reads.

Second, the read-scope. The worker's permission checker is pinned to the scan root with with_read_scope(scan_root). Every path argument is validated before a read runs. The logic is read_scope_allows in crates/lib/src/permissions/mod.rs. Concretely, it denies:

  • A path that canonicalizes outside the scan root.
  • A symlink whose target resolves outside the root. The check canonicalizes the target, not the link, so a symlink named notes.md that points at ~/.ssh/id_rsa is rejected.
  • Any hidden path component: .env, .git/config, a dot-prefixed directory. These hold local secrets and sit outside the intended scan surface.

A third confinement is easy to miss. A worker is not a subprocess or a second binary. It is an in-process run of the same query engine agent-code uses interactively, over whatever provider you configured. EngineAgent builds it with a hardened config: permission prompts off, and end-of-turn background memory extraction off. That last one matters. A worker that pulled facts out of the scanned repository into the operator's persistent memory store would be a quiet exfiltration channel. agent security-scan turns it off.

The glob pattern check is worth one more note. A glob is joined onto the scan root, so an absolute pattern or one with .. would escape. The check that rejects those does not rely on Path::is_absolute, which is platform-dependent: a Unix-style /etc/** is not absolute on Windows. It tests for a leading separator, a drive prefix, and a .. component directly, so the same rule holds on every host.

Recursion is the interesting part

Grep and Glob take a directory and recurse below it. They reach files that were never a path argument the gate saw. The per-argument check is not enough on its own, so each recursive tool is confined separately.

Glob filters every result through the same read-scope check, so a **/* pattern cannot enumerate .env under an in-scope root. ripgrep skips dotfiles by default. The plain-grep fallback is given explicit excludes, applied after any user include so they win. Both the pattern and the search path go after a -- terminator. A worker cannot smuggle -uu or --hidden as a pattern to re-enable hidden search. A user glob like .env* is neutralized by trailing exclusions that outrank it. This lives in crates/lib/src/tools/grep.rs and glob.rs.

One more consistency rule. The scan process runs from the scan root. A relative read or a default-directory grep resolves inside the scope, in both the tool and the gate. The two never disagree about where a relative path points.

Coverage you can audit

A scanner is only useful if you can trust a clean result. Two design choices make that trust earned.

The work queue is finite and deterministic. Selectors run with no model, so the set of files that reach a worker is knowable and reproducible. A given tree yields the same shards on every run. That is the opposite of an agent's unfalsifiable claim that it looked everywhere.

Worker failure is never a clean pass. A MAP or REDUCE worker can fail: a turn cap, a provider timeout, output that is not valid JSON. When that happens the scan increments worker_failures and the process exits 3, EXIT_INCOMPLETE_COVERAGE, distinct from the exit-2 code used for findings over threshold. Zero findings plus a nonzero exit means the analysis did not complete. Do not read it as clean. The exit logic is in crates/cli/src/security_scan.rs.

Malformed reducer output cannot erase real findings. The reducer reply is parsed strictly. If any finding or any attack chain fails to deserialize, the scan keeps the pre-reduce findings from the MAP stage and marks the reduce untrusted. A garbled reduce reply downgrades to incomplete coverage. It never turns a real P0 into a clean exit.

Incremental runs hold the same line. The engine caches per-file findings and re-maps only files changed since the last scanned commit. When the scan target is a subdirectory of a larger git repository, git reports paths relative to the repository top level. The engine rebases those paths onto the scan root before use. A changed file is never silently skipped because a path did not line up.

The cache is out of reach of the code under analysis. It lives in the user cache directory, keyed by the sha256 of the canonical repo path, never inside the target tree. A scanned repository cannot ship a poisoned cache that sets a base commit to skip every file. The scan never writes into the tree it reads. State advances only after a clean, complete run on an unmodified working tree. A dirty tree or a worker failure cannot seed a blind spot for the next run.

Running it

# Scan a repository, emit JSON, gate CI on P1 and above.
agent security-scan ./service --format json --severity-threshold P1

# Re-scan only what changed since the last scanned commit.
agent security-scan --incremental

Output is JSON or Markdown. The exit code gates CI: 2 for findings at or above the threshold, 3 for incomplete coverage, 0 only when every shard was analyzed clean. It is provider-agnostic. Point it at whatever model you run. All of this is in the 0.24.0 release and later.

A finding is a small JSON object:

{
  "cwe": "CWE-89",
  "file": "api/users.py",
  "line_range": [42, 42],
  "severity": "P0",
  "confidence": 0.92,
  "title": "SQL injection in user lookup",
  "exploit_preconditions": "unauthenticated request reaches the endpoint",
  "evidence": "cursor.execute(\"SELECT ... WHERE id = '%s'\" % request.args['id'])"
}

An attack chain is a second object type. It references its member finding ids and carries its own combined severity. That combined severity lets a chain gate CI even when no single member does.

What it does not do yet

The scanner is new, and honest framing matters more than polish.

Findings are statically gated. Each carries a severity, a confidence, and explicit preconditions, and must clear a false-positive gate inside the MAP worker. There is no runtime reproduction yet. A sandboxed per-finding repro stage, which would turn a high-confidence report into a proven one, is the next milestone.

AST selection covers Python and JavaScript. Other languages fall back to lexical matching. The selector set is curated and ships with the security profile. Having an agent study a repo and author selectors tuned to it is on the roadmap.

Security scanning is the first profile on a task-agnostic engine. The same plan, shard, map, reduce, gate backbone is built to carry code review, dead-code detection, and dependency audits.

Why we build it in the open

We run this against our own repositories. Avala produces the ground-truth training datasets behind autonomous vehicles and robotics. A missed vulnerability in that pipeline has real consequences, so whole-repo analysis is operational for us, not a demo.

Open tools get audited. If you see a way past the confinement, the code is right there to read: the read-scope in crates/lib/src/permissions/mod.rs, the worker setup in crates/lib/src/amr/agent.rs, the recursive-tool handling in crates/lib/src/tools/grep.rs. Pull requests are welcome.

If you find a vulnerability in an Avala system, our bug bounty pays for it. Report intake is at security.avala.ai/submit, with magic-link auth and a private thread per report. Full scope, rules, and reward tiers are at security.avala.ai/bounty.

Help us find the next one.