[Bug] Auto-accept edits not functioning; preferring unix tools over built-in Edit tool

Bug Description
1) Claude Code does not auto-accept edits even when I am in that mode. I have to manually approve every file edit.
2) It's favouring using unix tools rather than the in-built Edit tool for file modification using even more of my context window unecessarily.

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 2.0.44
• Feedback ID: 5b6b3489-b748-4219-851e-3eb2977ece7e

Errors

[{"error":"Error: Tool mcp__serena__search_for_pattern not found\n    at EqQ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1268:508)\n    at U$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:19414)\n    at Ne (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:42814)\n    at h9 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38355)\n    at Vl (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38283)\n    at j$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38137)\n    at AU (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:35216)\n    at PB (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:4841)\n    at H5 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:32461)\n    at Q.updateContainer (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:111:1827)","timestamp":"2025-11-18T15:05:34.734Z"},{"error":"Error: Tool mcp__serena__search_for_pattern not found\n    at EqQ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1268:508)\n    at U$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:19414)\n    at Ne (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:42814)\n    at h9 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38355)\n    at Vl (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38283)\n    at j$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38137)\n    at AU (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:35216)\n    at PB (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:4841)\n    at H5 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:32461)\n    at Q.updateContainer (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:111:1827)","timestamp":"2025-11-18T15:05:34.734Z"},{"error":"Error: Tool mcp__serena__search_for_pattern not found\n    at EqQ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1268:508)\n    at U$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:19414)\n    at Ne (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:42814)\n    at h9 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38355)\n    at Vl (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38283)\n    at j$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38137)\n    at AU (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:35216)\n    at PB (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:4841)\n    at H5 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:32461)\n    at Q.updateContainer (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:111:1827)","timestamp":"2025-11-18T15:05:34.734Z"},{"error":"Error: Tool mcp__serena__find_symbol not found\n    at EqQ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1268:508)\n    at U$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:19414)\n    at Ne (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:42814)\n    at h9 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38355)\n    at Vl (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38283)\n    at j$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:38137)\n    at AU (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:35216)\n    at PB (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:4841)\n    at H5 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:32461)\n    at Q.updateContainer (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:111:1827)","timestamp":"2025-11-18T15:05:34.756Z"},{"error":"Error: Tool mcp__serena__search_for_pattern not found\n    at EqQ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1268:508)\n    at U$ (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:105:19414)\n    at Ne (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:107:42814)\n    at h9 (

Note: Error logs were truncated.