Inconsistent Edit/Write permission behavior in accept-edits mode

Description

Edit/Write tool permissions behave inconsistently within a single session, even when "accept edits" mode is enabled. Some edits are auto-accepted while others require manual approval, with no apparent pattern.

Evidence from session analysis

Analyzed session 5832c201-6a20-4117-b326-3df09fca76f3 and found inconsistent timing between tool_use and user response:

| # | Tool | File | Delay | Behavior |
|---|------|------|-------|----------|
| 1 | Write | .claude/skills/TDDWorkflow/references/TypeScriptTestConfig.md | ~6 sec | Manual approval |
| 2 | Edit | CLAUDE.md | ~0.05 sec | Auto-accepted |
| 3 | Edit | .claude/skills/TDDWorkflow/SKILL.md | ~5.8 sec | Manual approval |

The ~6 second delays indicate waiting for user input, while ~0.05 sec indicates auto-acceptance. This happened within the same session with accept-edits mode enabled.

Environment

• Claude Code version: 2.1.7
• OS: macOS (Darwin 25.2.0)
• Terminal: Cursor IDE integrated terminal (issue was observed here)
• Also tested: Warp terminal (could not reproduce - worked correctly)

Settings checked

Reviewed all settings files - no Edit/Write specific permission rules found:

• ~/.claude/settings.json - only statusLine and hooks
• .claude/settings.json - only Bash permissions and PostToolUse hooks
• .claude/settings.local.json - only WebSearch and Skill permissions

Steps to reproduce

Unable to reliably reproduce. The issue occurred once and then worked correctly in subsequent sessions in both Cursor and Warp terminals.

Expected behavior

When accept-edits mode is enabled, all Edit/Write operations should be auto-accepted consistently.

Actual behavior

Some Edit/Write operations require manual approval while others are auto-accepted within the same session, despite accept-edits mode being enabled.

Additional context

• The issue may be related to running Claude Code in Cursor's integrated terminal
• Could be a session state corruption issue
• First observed: 2025-01-15 ~09:38 UTC