Handle generate config errors cleanly

[httpdss]

Summary

• Add GenerateConfigError for expected structure config load/shape failures.
• Load and validate structure YAML before creating backup/output directories, so invalid config does not leave partial side effects.
• Report missing files, invalid YAML, read errors, and top-level non-mapping YAML as clean ❗ ... errors with exit code 1 and no traceback.
• Preserve MCP generate behavior by converting clean CLI SystemExit failures into string errors for MCP callers.

Verification

• pre-commit run --all-files passed
• pytest -q passed: 195 passed
• git diff --check passed
• Ad-hoc verification script /tmp/hermes-verify-structkit-generate-clean-errors-* passed for invalid YAML, top-level non-mapping YAML, and missing file; it verified exit code 1, no Traceback, and no output directory side effects. Script was removed after execution.

Closes #164