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Cdxml fixes

R requested to merge cdxml_fixes into containerize

This MR refactors CDXML writing operations.

Testing:

  1. Checkout/pull the containerize branch. Use make chem-v2-all-test to generate SMILES and check the Indigo metrics at the command line.
  2. From main directory, copy outputs/All/generated_smiles//smiles.txt to ./SMILES-TEST.txt
  3. Checkout/pull this branch (cdxml_fixes), and repeat the first step.
  4. Run diff ./SMILES-TEST.txt <path-to-newer-smiles.txt in output/All/...> and check that Indigo metrics have not been affected compared to Step 1.
  5. Check that the output CDXML files (single, page, whole document) render correctly.

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