[Bug] Wildcard permissions don't supersede specific permissions in system prompt

Bug Description
Title: Redundant specific permissions accumulate in system prompt after wildcard permissions added

Description:

When a wildcard permission like Bash(gh:*) is configured in .claude/settings.local.json, previously-approved specific commands (e.g., Bash(gh pr create --title "..." --body "...")) continue to appear in the system prompt's allowed tools list.

Steps to reproduce:

1. Start with no gh permissions
2. Run gh pr create - approve when prompted (specific command gets added)
3. Run different gh commands - approve each (more specific entries accumulate)
4. Edit .claude/settings.local.json to add Bash(gh:*)
5. Start new session
6. Observe system prompt still contains all the specific gh pr create --title "..." --body "..." entries

Expected behavior:

Wildcard permissions should supersede specific permissions. When Bash(gh:*) is present, specific gh command entries should be removed or at minimum not included in the system prompt.

Actual behavior:

Both wildcard and all historical specific permissions are included in the system prompt, consuming context unnecessarily.

Impact:

• Wastes context window with redundant permission entries
• Some entries include full command bodies (heredocs with PR descriptions), adding significant bloat
• In my case, I see entries like Bash(gh pr create --title "feat: Add FredCollector MCP server" --body "$(cat <<''EOF''... with multi-line PR bodies

Environment:

• Claude Code (CLI)
• Ubuntu 24
• Permissions stored in .claude/settings.local.json

Environment Info

• Platform: linux
• Terminal: vscode
• Version: 2.0.54
• Feedback ID: f786bd80-bc80-4bad-86fd-2b9c7ec2eb67

Errors

[{"error":"Error\n    at NO (/$bunfs/root/claude:27:1143)\n    at <anonymous> (/$bunfs/root/claude:32:10056)\n    at emit (node:events:92:22)\n    at endReadableNT (internal:streams/readable:862:50)\n    at processTicksAndRejections (native:7:39)\n    at request (/$bunfs/root/claude:34:2147)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-11-27T12:28:57.013Z"},{"error":"Error\n    at NO (/$bunfs/root/claude:27:1143)\n    at <anonymous> (/$bunfs/root/claude:32:10056)\n    at emit (node:events:92:22)\n    at endReadableNT (internal:streams/readable:862:50)\n    at processTicksAndRejections (native:7:39)\n    at request (/$bunfs/root/claude:34:2147)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-11-27T12:28:57.017Z"},{"error":"Error\n    at NO (/$bunfs/root/claude:27:1143)\n    at <anonymous> (/$bunfs/root/claude:32:10056)\n    at emit (node:events:92:22)\n    at endReadableNT (internal:streams/readable:862:50)\n    at processTicksAndRejections (native:7:39)\n    at request (/$bunfs/root/claude:34:2147)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-11-27T12:28:57.151Z"},{"error":"Error\n    at NO (/$bunfs/root/claude:27:1143)\n    at <anonymous> (/$bunfs/root/claude:32:10056)\n    at emit (node:events:92:22)\n    at endReadableNT (internal:streams/readable:862:50)\n    at processTicksAndRejections (native:7:39)\n    at request (/$bunfs/root/claude:34:2147)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-11-27T12:28:57.178Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (/$bunfs/root/claude:12:370)\n    at WaI (/$bunfs/root/claude:4240:17094)\n    at call (/$bunfs/root/claude:1456:912)\n    at call (/$bunfs/root/claude:1452:5768)\n    at rt1 (/$bunfs/root/claude:2161:20843)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-11-27T12:30:27.078Z"}]