Issues

• ci: CodeQL quality noise: 68 of 100 open alerts are cs/path-combine (mostly tests), and every PR emails the owner 'CodeQL found more than 20 potential problems'

  area:packagingP1
  Raaif-Yousuf/DNA-Entropy-Graph#653 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• tooling: check_totest_format passes a ToTest table row split across two lines

  area:docsP3
  Raaif-Yousuf/DNA-Entropy-Graph#652 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• tests: JobReconcilerTests polls HungCalls and IsActive in a real-time window; wait on ActiveRuns.Started

  area:cloudP3
  Raaif-Yousuf/DNA-Entropy-Graph#647 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• settings: Advanced group (image overrides, fake-cloud indicator, reset settings) (#104)

  area:appP3
  Raaif-Yousuf/DNA-Entropy-Graph#644 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.3 daily-use polish

• settings: Notifications group (notify, open folder, open results when done) (#104)

  area:appP2
  Raaif-Yousuf/DNA-Entropy-Graph#643 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.3 daily-use polish

• settings: Files group (app data folder, inputs cache, logs) (#104)

  area:appP3
  Raaif-Yousuf/DNA-Entropy-Graph#642 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.3 daily-use polish

• settings: External viewers group (IGV path and port, Geneious path) (#104)

  area:appP2
  Raaif-Yousuf/DNA-Entropy-Graph#641 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.3 daily-use polish

• settings: Run defaults group edits the same stores New run reads (#104)

  area:appP1
  Raaif-Yousuf/DNA-Entropy-Graph#640 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.3 daily-use polish

• app: diagnostics withheld-job-id rewrite corrupts text for short/digit ids; escaped JSON ids (follow-up to #626)

  area:appP2
  Raaif-Yousuf/DNA-Entropy-Graph#637 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• cloud: guide an ineligible or free-trial account to a quota request (deep link, justification, FREE_TRIAL_NO_GPU)

  area:cloudP2
  Raaif-Yousuf/DNA-Entropy-Graph#636 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• cloud: request GPU quota with quotaInfos.get eligibility and quotaPreferences.create

  area:cloudP1
  Raaif-Yousuf/DNA-Entropy-Graph#635 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• cloud: apply the per-attempt request cap to Compute, IAM, ServiceUsage and Billing, and pin it on every Storage call site (from #600)

  area:cloudP3
  Raaif-Yousuf/DNA-Entropy-Graph#631 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• cloud: clean up the empty duplicate bucket a cut EnsureBucketAsync leaves behind

  area:cloudP3
  Raaif-Yousuf/DNA-Entropy-Graph#630 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• tooling: primary-checkout git guard follow-ups (Windows git timeout hang, comment-apostrophe bypass, smaller gaps)

  area:packagingP2
  Raaif-Yousuf/DNA-Entropy-Graph#629 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• app: Settings page shows its title twice

  area:uxP3
  Raaif-Yousuf/DNA-Entropy-Graph#627 · Filter by author Raaif-Yousuf opened on Oct 3, 2026
  1

• app: Save diagnostics refuses on a real profile (leak check fires), so no zip is produced

  area:appP1
  Raaif-Yousuf/DNA-Entropy-Graph#626 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• app: accounts.json locked at launch shows signed-out with no message and never refreshes

  area:cloudP3
  Raaif-Yousuf/DNA-Entropy-Graph#624 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• DECISION: should 'resources list' include buckets by default?

  area:cloudDECISIONP3
  Raaif-Yousuf/DNA-Entropy-Graph#622 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.1 walking skeleton

• packaging: cloud-canary.yml needs a non-user credential (blocked on owner)

  area:cloudP3
  Raaif-Yousuf/DNA-Entropy-Graph#621 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.1 walking skeleton

• cloud: accounts.json load-modify-save loses an update across processes

  area:cloudP3
  Raaif-Yousuf/DNA-Entropy-Graph#620 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• cloud: align cloud_gpu_test.ps1 -Apply vm create args with CloudCli's real flags

  area:cloudP2
  Raaif-Yousuf/DNA-Entropy-Graph#619 · Filter by author Raaif-Yousuf opened on Oct 3, 2026 · v0.1 walking skeleton
  1

• tooling: an orchestrator subagent's cwd gets pinned into a finished worktree Sonnet's worktree, and block_agent_dispatch_in_worktree then blocks every further dispatch

  area:packagingP1
  Raaif-Yousuf/DNA-Entropy-Graph#618 · Filter by author Raaif-Yousuf opened on Oct 3, 2026
  1

• DECISION: one DLVM image family for CPU and GPU VMs; --gpus only when expected

  area:cloudDECISIONP3
  Raaif-Yousuf/DNA-Entropy-Graph#615 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• worker/app: result.json error.code can carry a third-party exception's free-text .code into the diagnostics zip

  area:workerP2
  Raaif-Yousuf/DNA-Entropy-Graph#613 · Filter by author Raaif-Yousuf opened on Oct 3, 2026

• app: GenBank validation still accepts a stray ) feature line and a header // the worker refuses

  area:appP3
  Raaif-Yousuf/DNA-Entropy-Graph#611 · Filter by author Raaif-Yousuf opened on Oct 3, 2026