[BUG] Auto mode classifier denies routine user-requested actions since ~2.1.268 with no in-session override; forced us into bypassPermissions

What's wrong?

Auto mode has become unusable for long-running agent work since roughly 2.1.268. We run several Claude Code sessions in parallel on real engineering lanes (multi-repo PRs, deploy checks, Slack/GitHub automation). The classifier now denies ordinary, user-requested actions often enough that sessions stall partway through. Tokens are spent getting to the blocked step, and the agent then hands the human a long list of commands to run manually, which defeats the reason we run agents at all.

There is no way to override a denial from inside the session. The user typing "I authorize this" or "YES do it" in chat does not clear it. The denial text also forbids the agent from reaching the same outcome another way, so the only remedies are:

• stop and ask the human to run the command themselves, or
• hand-write permission rules for every new shape of command.

For us this became unbearable, so we switched defaultMode to bypassPermissions (--dangerously-skip-permissions). That is strictly worse for safety: we went from a model-side check that was too strict to no model-side check at all. Our own PreToolUse hooks now carry the whole load.

Measured on one workstation (local transcript aggregate, counts only)

| Versions | First seen | Tool calls | Auto-mode denials | Per 1k calls |
| ----------------- | ------------------ | ---------- | ----------------- | ------------ |
| 2.1.220–2.1.250 | 2026-07-26 → 08-28 | ~13,900 | 11 | ~0.8 |
| 2.1.251–2.1.267 | 08-28 → 09-10 | ~57,100 | 106 | ~1.9 |
| 2.1.268–2.1.274 | 09-11 → 09-17 | ~20,600 | 76 | ~3.7 |
| 2.1.278 | 09-19 | 7,615 | 40 | 5.3 |
| 2.1.280 | 09-22 | 1,456 | 13 | 8.9 |
| 2.1.281–2.1.282 | 09-24 | 7,862 | 33 | 4.2 |
| 2.1.283 (current) | 09-25 | 4,435 | 33 | 7.4 |

A denial rate per call understates the damage: a single denial usually ends the lane for that session, and the number of distinct sessions hitting at least one denial per version rose from 1 to 7–12.

Most frequent reason tags since 2.1.268: Production Reads, Credential Exploration, Self-Modification, Modify Shared Resources, Irreversible Local Destruction, Interfere With Workloads, Remote Shell Writes, External System Writes, Auto-Mode Bypass, CI Bypass, Merge Without Review.

Concrete examples from today's session (2.1.283), all explicitly requested by the user in chat

1. [Self-Modification] on reading a public GitHub issue template. gh api repos/anthropics/claude-code/contents/.github/ISSUE_TEMPLATE/... is a read of a public repo, and it was denied while the agent was preparing this issue.
2. [Self-Modification] on the user's own settings change. The user asked to switch defaultMode in ~/.claude/settings.json and confirmed in chat ("YES LET'S FLIP MODE"). The edit was denied, so the user has to make it by hand.
3. [External System Writes] / [Credential Exploration] on posting to the user's own Slack workspace. The user asked, several times and in capitals, for a setup guide to be posted to their own team channel. Every token route was denied, including a script that reads the secret in-process and never prints it. The agent ended up asking the user to run commands, which is exactly what they pay to avoid.
4. [Production Reads] on read-only production health checks during deploy verification that the user's own runbook mandates.

What should happen?

• An explicit, in-session user confirmation ("yes, do it") should be able to clear a denial for that specific action. Today the classifier ignores the user who is sitting at the keyboard.
• Read-only actions (public API reads, health checks) should not be treated as self-modification or production risk.
• A per-category allow list in settings, e.g. autoMode.allowCategories: ["External System Writes"], so one noisy category doesn't push users all the way to bypass mode.
• Changelog entries when classifier policy tightens, so regressions like this can be tied to a version.

Environment

• Claude Code 2.1.283, native install, Windows 11, defaultMode: auto (now bypassPermissions)
• Model: claude-opus-5-5
• Heavy use of PreToolUse hooks and parallel sessions

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