Critical gaps across all dimensions. Tool definitions are inferred from compact_tool.py rather than explicitly registered with schemas. Only 1 of 5 tools has a visible input schema (extract_structures_via_decimer_api). Descriptions are present but generic (10-50 chars), lacking WHEN/WHY context. No parameter descriptions visible for most tools. No output schemas documented. modify_molecule and render_cdxml_files lack any visible input specification. The audit_toolkit_interfaces.py file is a code analysis utility, not a tool definition registry. No evidence of error handling, validation, or recovery guidance.

• Create explicit tool registration with full JSON Schema for all 5 tools. For modify_molecule and render_cdxml_files, define input parameters (e.g., modification_type enum, output_format enum) with type, description, and constraints.
• Expand tool descriptions to 100-200 chars following the pattern: WHAT (action), WHEN (use case), WHAT IT RETURNS (output type). Example: 'Extract chemical structures from an image using DECIMER API. Call this first to identify molecules before modifying them. Returns a list of detected structures with SMILES strings and confidence scores.'
• Add parameter descriptions for all inputs. For specification_path, document format (JSON schema example). For output_path, clarify file extension and overwrite behavior. For modify_molecule, enumerate valid modification types.
• Document output schemas for each tool. Include field names, types, and whether results are paginated. For extract_structures_via_decimer_api, specify the structure of each detected molecule object.
• Add error handling guidance. For invalid image paths, return 'File not found at {path}. Ensure the path is absolute or relative to the working directory.' For invalid specifications, return 'Invalid JSON in specification_path: {error}. Expected keys: [list expected keys]'.