feat: refactor system prompt sections from markdown to XML format

[roomote]

Summary

This PR addresses Issue #7424 by refactoring the system prompt sections from markdown format to XML format, providing clearer semantic boundaries and better programmatic parsing capabilities.

Changes

Section Format Updates

• Replaced markdown separators (====) with XML <section name="SECTION_NAME"> tags
• Updated all section files to use the new XML format:
  • tool-use.ts: Now uses <section name="TOOL USE">
  • modes.ts: Now uses <section name="MODES">
  • capabilities.ts: Now uses <section name="CAPABILITIES">
  • rules.ts: Now uses <section name="RULES">
  • system-info.ts: Now uses <section name="SYSTEM INFORMATION">
  • objective.ts: Now uses <section name="OBJECTIVE">
  • markdown-formatting.ts: Now uses <section name="MARKDOWN RULES">
  • mcp-servers.ts: Now uses <section name="MCP SERVERS">

Tool Description Format Updates

• Converted all tool descriptions from markdown headers (## toolname) to XML format (<tool name="toolname">)
• Updated 20+ tool description files including:
  • Core tools: read_file, write_to_file, execute_command, etc.
  • Search tools: search_files, codebase_search, list_files
  • Interaction tools: ask_followup_question, attempt_completion, switch_mode
  • MCP tools: use_mcp_tool, access_mcp_resource
  • And many more...

Test Updates

• Updated test expectations to match the new XML format
• Updated all test snapshots to reflect the new structure
• All tests are passing

Benefits

1. Better Semantic Structure: XML tags provide clear semantic boundaries between different types of content
2. Easier Parsing: XML structure is easier to programmatically parse and manipulate than markdown separators
3. Improved Validation: XML format allows for better structure validation
4. Consistency: All sections and tools now follow a consistent XML-based format
5. Future-proof: Easier to extend with additional attributes or nested structures if needed

Testing

• ✅ All unit tests pass
• ✅ Linting passes
• ✅ Type checking passes
• ✅ Backward compatibility maintained (functionality unchanged, only format updated)

Important Note

As mentioned in the issue, the tool call functionality (which uses XML tags like <tool_name>) was NOT touched - only the system prompt structure was refactored.

Fixes #7424

---

Important

Refactor system prompt sections and tool descriptions from markdown to XML format for improved semantic clarity and parsing, updating test snapshots accordingly.

• Behavior:
  • Refactor system prompt sections from markdown to XML format for better semantic clarity and parsing.
  • Update test snapshots in system-prompt.spec.ts to reflect XML structure.
• Tool Descriptions:
  • Convert tool descriptions from markdown headers to XML format in over 20 files, including read_file, write_to_file, execute_command, etc.
• Testing:
  • Update test expectations and snapshots to match XML format.
  • All tests pass, ensuring backward compatibility.

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[roomote]

Reviewing my own code is like debugging in a mirror - everything looks backward but the bugs are still mine.

[roomote]

Is this intentional? I notice this tool uses an <important> tag for critical notes while other tools embed important information directly in the <description> tag. Could we consider standardizing this approach across all tools for consistency?

For example, other tools include warnings like "IMPORTANT: You can read a maximum of 5 files..." directly in the description, but here we have a separate <important> tag.

[roomote]

Similar to my comment on attempt-completion.ts - this tool uses both <description> and <important> tags, creating a mixed content structure. While this provides good separation of concerns, it differs from the pattern used in most other tools.

Could we consider either:

1. Moving all tools to use the <important> tag pattern for consistency, or
2. Embedding the important notes in the description like other tools do?