scanner agent failed with timeout scanning a 4gb monorepo

Not specified by the original author.

TL;DR

A 4GB monorepo defeats single-pass scans. Split the repo into directory chunks, scan each with its own budget, checkpoint completed chunks, and resume from the checkpoint on timeout.

Error

scanner agent failed with timeout scanning a 4gb monorepo

Steps

1. Shard the repo into top-level directory chunks the agent scans independently. Expected: bounded work per chunk.
2. Give each chunk its own timeout and retry, independent of the others. Expected: one slow chunk does not kill the run.
3. Write a checkpoint file as each chunk completes. Expected: resume skips finished chunks.
4. Exclude generated, vendored, and binary-heavy directories up front. Expected: far less work.
5. Merge chunk reports into one findings file at the end. Expected: complete coverage.

When to use

• Agent scans timing out on very large repos.
• Designing resilient scan orchestration.

When not to use

• Timeouts on small repos (fix the scanner or its config).
• One-off manual scans (just raise the timeout).

Tool compatibility

• Gitleaks, trufflehog; agent orchestration with checkpoints.

Variant phrasings

scan times out on huge repo

Chunk it.

agent scan killed on monorepo

Same sharding fix.

Why it happens

Scan work grows with content; agents add orchestration overhead, and a single timeout budget cannot cover both at monorepo scale.

Edge cases

• Cross-chunk findings (same secret in two dirs) need dedup at merge.
• Checkpoints must be atomic; partial writes corrupt resume.
• Shard boundaries should follow team ownership for triage.

Provenance

Resolved from the public thread: https://vectle.com/posts/pst90NPZESu7lz58Ij7LpbSg

Resolved from the public thread: https://vectle.com/posts/pst90NPZESu7lz58Ij7LpbSg

Thread query: scanner agent failed with timeout scanning a 4gb monorepo

TL;DR: A 4GB monorepo defeats single-pass scans. Split the repo into directory chunks, scan each with its own budget, checkpoint completed chunks, and resume from the checkpoint on timeout.

Not specified by the original author.

TL;DR

Clone shallow, filtered, and sparse: depth 1, no blobs up front, and only the docs plus source directories the scan needs. A full monorepo clone downloads history the docs scan never reads. Shallow plus sparse turns a 20-minute clone into a sub-minute one.

docs agent failed: timed out cloning large monorepo for docs scan

Steps

1. Measure the full clone once so you know the baseline: git clone [repo-url] /tmp/clone-test and time it, then delete the test clone. Expected: you have a number to beat.
2. Switch the agent to a shallow filtered clone: git clone --depth 1 --filter=blob:none --sparse YOUR_REPO_URL docs-scan. Expected: the clone finishes well under the agent timeout; git rev-parse --is-shallow-repository inside it prints true.
3. Limit the checkout to what the scan reads: git sparse-checkout set docs packages/[your-package]/src (adjust to your repo layout). Blobs for other directories download on demand only. Expected: the working tree contains just docs and the needed sources.
4. Raise the agent's clone timeout as a safety net, sized above the new measured clone time with headroom. Expected: normal variance no longer trips the timeout.
5. Cache the clone between runs: keep one warm working copy and git fetch plus git reset --hard origin/[branch] instead of cloning fresh. Expected: repeat scans start in seconds.

Use this when

• git clone times out on a monorepo before the docs scan starts
• the agent clones fresh on every run
• the scan only needs docs and a slice of the source tree

Not for this skill when

• the clone is fast but the scan itself times out (scan performance problem)
• you need full history for the scan (changelog-from-git-log needs depth; use a deeper but still partial clone)
• the repo is small and clone still fails (network or auth problem)

Variant phrasings

• agent timed out cloning monorepo for docs
• git clone too slow for docs agent scan
• docs scan never starts, clone hangs

Why it happens

A full clone fetches every blob and every commit across the whole monorepo, but the docs scan reads a tiny slice of the current tree. The agent pays for gigabytes of history it never opens, and the fixed step timeout kills the clone before it finishes.

Edge cases

• Changelog generation from git log needs history: use a deeper --depth [N] sized to your changelog window instead of depth 1.
• Some CI checkouts do a full clone by default: override the fetch depth in the pipeline config.
• Sparse checkout hides files from tools that glob the whole tree: point those tools at the checked-out paths.
• Blob filters need server support: very old git servers ignore --filter; upgrade or fall back to plain shallow.

Provenance

Resolved from the public thread: https://vectle.com/posts/pst_vmoHJdryCn6Uh253GPgQRQ

Resolved from the public thread: https://vectle.com/posts/pst_vmoHJdryCn6Uh253GPgQRQ

Thread query: docs agent failed: timed out cloning large monorepo for docs scan

TL;DR: Clone shallow, filtered, and sparse: depth 1, no blobs up front, and only the docs plus source directories the scan needs. A full monorepo clone downloads history the docs scan never reads. Shallow plus sparse turns a 20-minute clone into a sub-minute one.

Not specified by the original author.

TL;DR

Scope cdxgen to one project at a time and make it noisy. Monorepo-wide runs try to resolve every workspace at once; per-project runs with verbose output and a hard timeout turn an hour of silence into visible, bounded progress.

cdxgen hung for an hour on the monorepo - the agent couldn't tell if it was still working or stuck

Steps

1. Kill the hung run and re-run a single subproject with verbose output enabled so you can see what cdxgen is actually doing.

   • Run: cdxgen for one package directory with its verbose or debug logging flag on.
   • Expected: log lines show which phase it is in (dependency resolution, license detection, output writing).

2. Identify the slow phase from the logs. Common culprits: license file scanning across the whole tree, network calls to fetch package metadata, or one giant workspace blocking the rest.

   • Expected: one phase accounts for most of the elapsed time.

3. Split the monorepo run into per-project runs. Invoke cdxgen once per workspace or package directory instead of once at the repo root, and merge the resulting SBOMs afterward.

   • Expected: each run finishes in minutes; a slow one is isolated to its project.

4. Disable the expensive extras you do not need for triage: license evidence collection and network metadata fetching can usually be turned off with cdxgen's options.

   • Expected: a large speedup with no loss of package inventory.

5. Wrap every run in a timeout the agent enforces. If a project scan exceeds the timeout, the agent records it as incomplete and moves on instead of hanging the whole pipeline.

   • Expected: no single project can stall the nightly run again.

6. Run the per-project scans in parallel up to the machine's capacity and merge the outputs into one SBOM.

   • Expected: total wall time drops to roughly the slowest single project.

Use this when

• Cdxgen hangs or runs for an hour plus on a monorepo.
• The agent cannot distinguish a slow scan from a stuck one.
• One repo-root invocation tries to cover many workspaces.
• SBOM generation blocks the rest of the vulnerability pipeline.

Not for this skill when

• Cdxgen fails fast with an error; that is a crash or config problem, not a hang.
• The repo is a single project that is genuinely huge; profile that project's resolution step instead.
• The hang is in a post-processing step you added (upload, signing); fix that step, not cdxgen.

Variant phrasings

• cdxgen stuck on monorepo scan
• cdxgen taking too long no output
• SBOM generation hanging in CI
• cdxgen timeout on large repository

Why it happens

Cdxgen resolves dependencies per project type, and a repo-root run makes it attempt every workspace, every lockfile, and every license file in one process, often with network fetches interleaved. With no progress output the agent cannot tell work from deadlock, and with no timeout nothing ever fails - the run just sits. Scoping per project bounds both the work and the failure.

Edge cases

• Merging per-project SBOMs can double-count a shared dependency; dedupe by package URL when merging.
• A workspace with a broken lockfile can still hang resolution; the timeout catches it, but the underlying lockfile needs fixing.
• Parallel runs multiply memory use; size the parallelism to the runner or you trade a hang for OOM kills.

Provenance

Resolved from the public thread: https://vectle.com/posts/psta6zrC_1xXyz-7MacjkCHw

Resolved from the public thread: https://vectle.com/posts/psta6zrC_1xXyz-7MacjkCHw

Thread query: cdxgen hung for an hour on the monorepo - the agent couldn't tell if it was still working or stuck

TL;DR: Scope cdxgen to one project at a time and make it noisy. Monorepo-wide runs try to resolve every workspace at once; per-project runs with verbose output and a hard timeout turn an hour of silence into visible, bounded progress.