/auto-mode-setup fails: removeFromPermissionsAllow[0] is not a rule string the removal offer could have produced

Bug: /auto-mode-setup fails with "removeFromPermissionsAllow[0] is not a rule string the removal offer could have produced"

Claude Code version: 2.1.238
OS: Linux (Ubuntu 24.04, EC2), kernel 6.17.0-1019-aws, x86_64
Surface: Claude Code CLI, interactive session

Steps to reproduce

1. In a project with a large, long-lived permissions config (project .claude/settings.json ~138 permissions.allow entries, .claude/settings.local.json ~1152 entries, user ~/.claude/settings.json 4 entries), run /auto-mode-setup.
2. Command prints local-command-stdout: Gathering data and drafting your auto-mode setup; back soon.
3. Command then fails with:

``
Auto-mode setup scan failed: removeFromPermissionsAllow[0] is not a rule string the removal offer could have produced.
``

Expected behavior

/auto-mode-setup completes and returns a drafted auto-mode configuration (or a proposed diff of permission rules to remove/add), or fails with an error that identifies which specific rule/entry triggered the problem.

Actual behavior

The command fails every time with the same internal-consistency error. Retrying (same session and a fresh invocation) reproduces the identical failure.

Investigation so far

• Checked all three applicable permissions.allow arrays (project .claude/settings.json, project .claude/settings.local.json, user ~/.claude/settings.json) for non-string entries — none found; every entry is a well-formed string.
• The error message implies the command computed a removeFromPermissionsAllow list internally and then validated element [0] against the set of rule strings it should be able to produce from the current config — and that validation failed. Since the on-disk config has no malformed entries, this looks like a bug in the command's own rule-generation/removal-offer logic (possibly related to the very large settings.local.json allow list, or to how rules from multiple settings files are merged/deduplicated before the removal offer is built) rather than corrupted user config.

Additional context

• Not project-specific in an obvious way, but this project's config is unusually large (1150+ local allow rules), which may be relevant to reproducing it.