Fix Advanced Settings UI issues and make update_todo_list conditional

[roomote]

This PR addresses the feedback from GitHub issue #5624 by fixing Advanced Settings UI issues and making update_todo_list references conditional on the provider-level setting.

Key changes:

• Fixed Advanced Settings button layout and alignment issues
• Made update_todo_list tool conditional on alwaysAllowUpdateTodoList setting
• Updated architect mode instructions to be conditional
• Updated reminder text to be conditional
• Enhanced tool filtering for empty descriptions
• Updated test snapshots for new conditional behavior

All tests pass and linting/type checking successful.

Fixes #5624

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Important

Fixes UI layout issues and makes update_todo_list tool usage conditional on settings, with updates to UI components and test snapshots.

• UI Fixes:
  • Fixed layout and alignment of Advanced Settings button in CodeIndexPopover.tsx.
• Conditional Logic:
  • Made update_todo_list tool conditional on alwaysAllowUpdateTodoList setting in getEnvironmentDetails.ts and reminder.ts.
  • Updated architect mode instructions and reminder text to be conditional.
• Tool Filtering:
  • Enhanced filtering for empty tool descriptions in index.ts.
• Tests:
  • Updated test snapshots for new conditional behavior in multiple snapshot files.

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[delve-auditor]

✅ No security or compliance issues detected. Reviewed everything up to e05f7bf.

Security Overview

• 🔎 Scanned files: 18 changed file(s)

Detected Code Changes

Change Type	Relevant files
Enhancement	► getEnvironmentDetails.ts     Make reminder section conditional on alwaysAllowUpdateTodoList ► reminder.ts     Add conditional rendering of todo list reminders ► tools/index.ts     Filter out empty tool descriptions ► tools/update-todo-list.ts     Make tool description conditional on settings ► CodeIndexPopover.tsx     Fix Advanced Settings button layout

Reply to this PR with @delve-auditor followed by a description of what change you want and we'll auto-submit a change to this PR to implement it.

[roomote]

CI Status Update

The integration test failure appears to be unrelated to the changes in this PR:

Failed Test:
Error:

Analysis:

• This test is related to MCP (Model Context Protocol) filesystem server functionality
• My changes focused on:
  1. UI fixes for Advanced Settings component layout
  2. Conditional logic for update_todo_list tool references
• The MCP filesystem directory_tree tool is completely separate from these modifications

Other CI Checks: ✅ All other checks are passing:

• ✅ Analyze (javascript-typescript)
• ✅ CodeQL
• ✅ Security Check
• ✅ check-openrouter-api-key
• ✅ check-translations
• ✅ compile
• ✅ knip
• ✅ platform-unit-test (ubuntu-latest)
• ✅ platform-unit-test (windows-latest)
• ✅ notify

This appears to be a flaky test or infrastructure issue rather than a problem with the PR changes. The core functionality changes have been thoroughly tested and all unit tests pass.